path: root/esample

#!/bin/sh

do_help() {
  cat <<EOF
  
Usage: esample [ -docsum | -article | -book | -protein | -gene | -taxon | -blast | -snp | -bioc | -flatfile | -gencode ]

EOF
}

do_docsum() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE DocumentSummarySet>
<DocumentSummarySet status="OK">
  <DocumentSummary>
    <Id>6301692</Id>
    <PubDate>1983 Apr</PubDate>
    <Source>Cell</Source>
    <Authors>
      <Author>
        <Name>Krasnow MA</Name>
        <AuthType>Author</AuthType>
      </Author>
      <Author>
        <Name>Cozzarelli NR</Name>
        <AuthType>Author</AuthType>
      </Author>
    </Authors>
    <LastAuthor>Cozzarelli NR</LastAuthor>
    <Title>Site-specific relaxation and recombination by the Tn3 resolvase: recognition of the DNA path between oriented res sites.</Title>
    <SortTitle>site specific relaxation and recombination by the tn3 resolvase recognition of the dna path between oriented res sites</SortTitle>
    <Volume>32</Volume>
    <Issue>4</Issue>
    <Pages>1313-24</Pages>
    <Lang>
      <string>eng</string>
    </Lang>
    <NlmUniqueID>0413066</NlmUniqueID>
    <ISSN>0092-8674</ISSN>
    <ESSN>1097-4172</ESSN>
    <PubType>
      <flag>Journal Article</flag>
    </PubType>
    <RecordStatus>PubMed - indexed for MEDLINE</RecordStatus>
    <PubStatus>4</PubStatus>
    <ArticleIds>
      <ArticleId>
        <IdType>pubmed</IdType>
        <IdTypeN>1</IdTypeN>
        <Value>6301692</Value>
      </ArticleId>
      <ArticleId>
        <IdType>pii</IdType>
        <IdTypeN>4</IdTypeN>
        <Value>0092-8674(83)90312-4</Value>
      </ArticleId>
      <ArticleId>
        <IdType>doi</IdType>
        <IdTypeN>3</IdTypeN>
        <Value>10.1016/0092-8674(83)90312-4</Value>
      </ArticleId>
      <ArticleId>
        <IdType>rid</IdType>
        <IdTypeN>8</IdTypeN>
        <Value>6301692</Value>
      </ArticleId>
      <ArticleId>
        <IdType>eid</IdType>
        <IdTypeN>8</IdTypeN>
        <Value>6301692</Value>
      </ArticleId>
    </ArticleIds>
    <History>
      <PubMedPubDate>
        <PubStatus>pubmed</PubStatus>
        <Date>1983/04/01 00:00</Date>
      </PubMedPubDate>
      <PubMedPubDate>
        <PubStatus>medline</PubStatus>
        <Date>1983/04/01 00:01</Date>
      </PubMedPubDate>
      <PubMedPubDate>
        <PubStatus>entrez</PubStatus>
        <Date>1983/04/01 00:00</Date>
      </PubMedPubDate>
    </History>
    <Attributes>
      <flag>Has Abstract</flag>
    </Attributes>
    <PmcRefCount>57</PmcRefCount>
    <FullJournalName>Cell</FullJournalName>
    <DocType>citation</DocType>
    <SortPubDate>1983/04/01 00:00</SortPubDate>
    <SortFirstAuthor>Krasnow MA</SortFirstAuthor>
  </DocumentSummary>
</DocumentSummarySet>
EOF
}

do_article() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE PubmedArticle>
<PubmedArticle>
  <MedlineCitation Status="MEDLINE" Owner="NLM">
    <PMID Version="1">6301692</PMID>
    <DateCompleted>
      <Year>1983</Year>
      <Month>06</Month>
      <Day>17</Day>
    </DateCompleted>
    <DateRevised>
      <Year>2019</Year>
      <Month>07</Month>
      <Day>05</Day>
    </DateRevised>
    <Article PubModel="Print">
      <Journal>
        <ISSN IssnType="Print">0092-8674</ISSN>
        <JournalIssue CitedMedium="Print">
          <Volume>32</Volume>
          <Issue>4</Issue>
          <PubDate>
            <Year>1983</Year>
            <Month>Apr</Month>
          </PubDate>
        </JournalIssue>
        <Title>Cell</Title>
      </Journal>
      <ArticleTitle>Site-specific relaxation and recombination by the Tn3 resolvase: recognition of the DNA path between oriented res sites.</ArticleTitle>
      <Pagination>
        <MedlinePgn>1313-24</MedlinePgn>
      </Pagination>
      <Abstract>
        <AbstractText Label="RESULTS">We studied the dynamics of site-specific recombination by the resolvase encoded by the Escherichia coli transposon Tn3.
The pure enzyme recombined supercoiled plasmids containing two directly repeated recombination sites, called res sites.
Resolvase is the first strictly site-specific topoisomerase.
It relaxed only plasmids containing directly repeated res sites; substrates with zero, one or two inverted sites were inert.
Even when the proximity of res sites was ensured by catenation of plasmids with a single site, neither relaxation nor recombination occurred.
The two circular products of recombination were catenanes interlinked only once.
These properties of resolvase require that the path of the DNA between res sites be clearly defined and that strand exchange occur with a unique geometry.</AbstractText>
        <AbstractText Label="SUMMARY">A model in which one subunit of a dimeric resolvase is bound at one res site,
while the other searches along adjacent DNA until it encounters the second site,
would account for the ability of resolvase to distinguish intramolecular from intermolecular sites,
to sense the relative orientation of sites and to produce singly interlinked catenanes.
Because resolvase is a type 1 topoisomerase, we infer that it makes the required duplex bDNA breaks of recombination one strand at a time.</AbstractText>
      </Abstract>
      <AuthorList CompleteYN="Y">
        <Author ValidYN="Y">
          <LastName>Krasnow</LastName>
          <ForeName>Mark A</ForeName>
          <Initials>MA</Initials>
        </Author>
        <Author ValidYN="Y">
          <LastName>Cozzarelli</LastName>
          <ForeName>Nicholas R</ForeName>
          <Initials>NR</Initials>
        </Author>
      </AuthorList>
      <Language>eng</Language>
      <GrantList CompleteYN="Y">
        <Grant>
          <GrantID>GM-07281</GrantID>
          <Acronym>GM</Acronym>
          <Agency>NIGMS NIH HHS</Agency>
          <Country>United States</Country>
        </Grant>
      </GrantList>
      <PublicationTypeList>
        <PublicationType UI="D016428">Journal Article</PublicationType>
        <PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType>
      </PublicationTypeList>
    </Article>
    <MedlineJournalInfo>
      <Country>United States</Country>
      <MedlineTA>Cell</MedlineTA>
      <NlmUniqueID>0413066</NlmUniqueID>
      <ISSNLinking>0092-8674</ISSNLinking>
    </MedlineJournalInfo>
    <ChemicalList>
      <Chemical>
        <RegistryNumber>0</RegistryNumber>
        <NameOfSubstance UI="D004269">DNA, Bacterial</NameOfSubstance>
      </Chemical>
      <Chemical>
        <RegistryNumber>0</RegistryNumber>
        <NameOfSubstance UI="D004278">DNA, Superhelical</NameOfSubstance>
      </Chemical>
      <Chemical>
        <RegistryNumber>0</RegistryNumber>
        <NameOfSubstance UI="D004279">DNA, Viral</NameOfSubstance>
      </Chemical>
      <Chemical>
        <RegistryNumber>EC 2.7.7.-</RegistryNumber>
        <NameOfSubstance UI="D009713">Nucleotidyltransferases</NameOfSubstance>
      </Chemical>
      <Chemical>
        <RegistryNumber>EC 2.7.7.-</RegistryNumber>
        <NameOfSubstance UI="D019895">Transposases</NameOfSubstance>
      </Chemical>
      <Chemical>
        <RegistryNumber>EC 5.99.1.2</RegistryNumber>
        <NameOfSubstance UI="D004264">DNA Topoisomerases, Type I</NameOfSubstance>
      </Chemical>
    </ChemicalList>
    <CitationSubset>IM</CitationSubset>
    <MeshHeadingList>
      <MeshHeading>
        <DescriptorName UI="D004264" MajorTopicYN="N">DNA Topoisomerases, Type I</DescriptorName>
        <QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName>
        <QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D004278" MajorTopicYN="N">DNA, Superhelical</DescriptorName>
        <QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D004279" MajorTopicYN="N">DNA, Viral</DescriptorName>
        <QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D009690" MajorTopicYN="Y">Nucleic Acid Conformation</DescriptorName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D009713" MajorTopicYN="N">Nucleotidyltransferases</DescriptorName>
        <QualifierName UI="Q000302" MajorTopicYN="N">isolation &amp; purification</QualifierName>
        <QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D010957" MajorTopicYN="N">Plasmids</DescriptorName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D011995" MajorTopicYN="Y">Recombination, Genetic</DescriptorName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D012091" MajorTopicYN="N">Repetitive Sequences, Nucleic Acid</DescriptorName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D013539" MajorTopicYN="N">Simian virus 40</DescriptorName>
      </MeshHeading>
      <MeshHeading>
        <DescriptorName UI="D019895" MajorTopicYN="N">Transposases</DescriptorName>
      </MeshHeading>
    </MeshHeadingList>
  </MedlineCitation>
  <PubmedData>
    <History>
      <PubMedPubDate PubStatus="pubmed">
        <Year>1983</Year>
        <Month>4</Month>
        <Day>1</Day>
      </PubMedPubDate>
      <PubMedPubDate PubStatus="medline">
        <Year>1983</Year>
        <Month>4</Month>
        <Day>1</Day>
        <Hour>0</Hour>
        <Minute>1</Minute>
      </PubMedPubDate>
      <PubMedPubDate PubStatus="entrez">
        <Year>1983</Year>
        <Month>4</Month>
        <Day>1</Day>
        <Hour>0</Hour>
        <Minute>0</Minute>
      </PubMedPubDate>
    </History>
    <PublicationStatus>ppublish</PublicationStatus>
    <ArticleIdList>
      <ArticleId IdType="pubmed">6301692</ArticleId>
      <ArticleId IdType="pii">0092-8674(83)90312-4</ArticleId>
      <ArticleId IdType="doi">10.1016/0092-8674(83)90312-4</ArticleId>
    </ArticleIdList>
  </PubmedData>
</PubmedArticle>
EOF
}

do_book() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE PubmedArticleSet>
<PubmedArticleSet>
  <PubmedBookArticle>
    <BookDocument>
      <PMID Version="1">21433338</PMID>
      <ArticleIdList>
        <ArticleId IdType="bookaccession">NBK19359</ArticleId>
      </ArticleIdList>
      <Book>
        <Publisher>
          <PublisherName>Cold Spring Harbor Laboratory Press</PublisherName>
          <PublisherLocation>Cold Spring Harbor (NY)</PublisherLocation>
        </Publisher>
        <BookTitle book="rv">Retroviruses</BookTitle>
        <PubDate>
          <Year>1997</Year>
        </PubDate>
        <AuthorList Type="editors">
          <Author>
            <LastName>Coffin</LastName>
            <ForeName>John M</ForeName>
            <Initials>JM</Initials>
          </Author>
          <Author>
            <LastName>Hughes</LastName>
            <ForeName>Stephen H</ForeName>
            <Initials>SH</Initials>
          </Author>
          <Author>
            <LastName>Varmus</LastName>
            <ForeName>Harold E</ForeName>
            <Initials>HE</Initials>
          </Author>
        </AuthorList>
        <Isbn>0879695714</Isbn>
      </Book>
      <ArticleTitle book="rv" part="A6253">Pathogenesis of HIV and SIV</ArticleTitle>
      <Language>eng</Language>
      <AuthorList Type="authors">
        <Author>
          <LastName>Fauci</LastName>
          <ForeName>AS</ForeName>
          <Initials>AS</Initials>
        </Author>
        <Author>
          <LastName>Desrosiers</LastName>
          <ForeName>RC</ForeName>
          <Initials>RC</Initials>
        </Author>
      </AuthorList>
      <PublicationType UI="D016454">Review</PublicationType>
      <Abstract>
        <AbstractText>Infections by viruses of the lentivirus genus, most notably human immunodeficiency virus type 1 (HIV-1), are characterized by remarkably complex interactions with the host and a chronic course of disease. Common features of diseases caused by lentiviruses include long and variable incubation periods, persistent viral replication, neurologic manifestations, and destruction of specific hematologic or immunologic cells (Desrosiers and Letvin 1987); some of these characteristics, particularly as they relate to nonprimate lentiviruses, are described in Chapter 10 All lentiviruses exhibit a common morphogenesis and morphology, a tropism for macrophages, extensive genetic and antigenic variability, and the presence of additional regulatory genes not found in other groups of retroviruses. Lentiviruses are not directly oncogenic, although the immune disorders they induce often permit the growth of certain neoplasms, such as lymphomas and Kaposi's sarcoma. Lentiviruses have been isolated from several animal species including sheep, goats, horses, cattle, cats, monkeys, and humans. HIV-1 and HIV-2 are the only known human lentiviruses. Infection of humans with HIV-1 causes a dramatic decline in the number of CD4+ T lymphocytes. When the number of these cells becomes low enough, opportunistic infections and neoplasms occur. Neurologic abnormalities, which occur in a majority of HIV-infected individuals, can be observed in the absence of other clinical manifestations (Fauci 1988). The HIV-related lentiviruses of nonhuman primates are collectively called simian immunodeficiency viruses (SIVs). Related but distinct SIVs have been isolated from several species of African monkeys. SIV and HIV will be referred to as primate lentiviruses; more distant relatives from other animal species will be referred to as nonprimate lentiviruses. As with HIV, infection of an appropriate host with SIV results in the decline of the absolute number of CD4+ T cells, an inversion of the CD4/CD8 T-cell ratio, neurologic abnormalities, and opportunistic infections (Simon et al. 1994).</AbstractText>
        <CopyrightInformation>Copyright © 1997, Cold Spring Harbor Laboratory Press.</CopyrightInformation>
      </Abstract>
      <Sections>
        <Section>
          <SectionTitle book="rv" part="A6254">Etiologic Agents</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6265">Cellular Targets of Infection</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6269">Course of Infection with HIV and SIV</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6284">Immunopathogenic Mechanisms of HIV Infection</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6304">Role of Lymphoid Organs in Immunopathogenesis</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6308">Pathogenesis of Kaposi's Sarcoma and Other Opportunistic Neoplasms</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6311">Tissue-Specific Disease and Organ System Failure</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6317">Immune Responses to HIV and SIV</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6324">Conclusions</SectionTitle>
        </Section>
        <Section>
          <SectionTitle book="rv" part="A6325">References</SectionTitle>
        </Section>
      </Sections>
    </BookDocument>
    <PubmedBookData>
      <History>
        <PubMedPubDate PubStatus="pubmed">
          <Year>2011</Year>
          <Month>3</Month>
          <Day>25</Day>
          <Hour>6</Hour>
          <Minute>0</Minute>
        </PubMedPubDate>
        <PubMedPubDate PubStatus="medline">
          <Year>2011</Year>
          <Month>3</Month>
          <Day>25</Day>
          <Hour>6</Hour>
          <Minute>0</Minute>
        </PubMedPubDate>
        <PubMedPubDate PubStatus="entrez">
          <Year>2011</Year>
          <Month>3</Month>
          <Day>25</Day>
          <Hour>6</Hour>
          <Minute>0</Minute>
        </PubMedPubDate>
      </History>
      <PublicationStatus>ppublish</PublicationStatus>
      <ArticleIdList>
        <ArticleId IdType="pubmed">21433338</ArticleId>
      </ArticleIdList>
    </PubmedBookData>
  </PubmedBookArticle>
</PubmedArticleSet>
EOF
}

do_protein() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE INSDSeq>
<INSDSeq>
  <INSDSeq_locus>AF480315_1</INSDSeq_locus>
  <INSDSeq_length>67</INSDSeq_length>
  <INSDSeq_moltype>AA</INSDSeq_moltype>
  <INSDSeq_topology>linear</INSDSeq_topology>
  <INSDSeq_division>INV</INSDSeq_division>
  <INSDSeq_update-date>25-JUL-2016</INSDSeq_update-date>
  <INSDSeq_create-date>31-DEC-2003</INSDSeq_create-date>
  <INSDSeq_definition>four-loop conotoxin preproprotein, partial [Conus purpurascens]</INSDSeq_definition>
  <INSDSeq_primary-accession>AAQ05867</INSDSeq_primary-accession>
  <INSDSeq_accession-version>AAQ05867.1</INSDSeq_accession-version>
  <INSDSeq_other-seqids>
    <INSDSeqid>gb|AAQ05867.1|AF480315_1</INSDSeqid>
    <INSDSeqid>gi|33320307</INSDSeqid>
  </INSDSeq_other-seqids>
  <INSDSeq_source>Conus purpurascens</INSDSeq_source>
  <INSDSeq_organism>Conus purpurascens</INSDSeq_organism>
  <INSDSeq_taxonomy>Eukaryota; Metazoa; Lophotrochozoa; Mollusca; Gastropoda; Caenogastropoda; Hypsogastropoda; Neogastropoda; Conoidea; Conidae; Conus</INSDSeq_taxonomy>
  <INSDSeq_references>
    <INSDReference>
      <INSDReference_reference>1</INSDReference_reference>
      <INSDReference_position>1..67</INSDReference_position>
      <INSDReference_authors>
        <INSDAuthor>Duda,T.F. Jr.</INSDAuthor>
        <INSDAuthor>Palumbi,S.R.</INSDAuthor>
      </INSDReference_authors>
      <INSDReference_title>Convergent evolution of venoms and feeding ecologies among polyphyletic piscivorous Conus species</INSDReference_title>
      <INSDReference_journal>Unpublished</INSDReference_journal>
    </INSDReference>
    <INSDReference>
      <INSDReference_reference>2</INSDReference_reference>
      <INSDReference_position>1..67</INSDReference_position>
      <INSDReference_authors>
        <INSDAuthor>Duda,T.F. Jr.</INSDAuthor>
        <INSDAuthor>Palumbi,S.R.</INSDAuthor>
      </INSDReference_authors>
      <INSDReference_title>Direct Submission</INSDReference_title>
      <INSDReference_journal>Submitted (04-FEB-2002) Naos Marine Lab, Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Ancon, Panama, Republic of Panama</INSDReference_journal>
    </INSDReference>
  </INSDSeq_references>
  <INSDSeq_comment>Method: conceptual translation supplied by author.</INSDSeq_comment>
  <INSDSeq_source-db>accession AF480315.1</INSDSeq_source-db>
  <INSDSeq_feature-table>
    <INSDFeature>
      <INSDFeature_key>source</INSDFeature_key>
      <INSDFeature_location>1..67</INSDFeature_location>
      <INSDFeature_intervals>
        <INSDInterval>
          <INSDInterval_from>1</INSDInterval_from>
          <INSDInterval_to>67</INSDInterval_to>
          <INSDInterval_accession>AAQ05867.1</INSDInterval_accession>
        </INSDInterval>
      </INSDFeature_intervals>
      <INSDFeature_quals>
        <INSDQualifier>
          <INSDQualifier_name>organism</INSDQualifier_name>
          <INSDQualifier_value>Conus purpurascens</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>isolate</INSDQualifier_name>
          <INSDQualifier_value>purpurascens-2c</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>db_xref</INSDQualifier_name>
          <INSDQualifier_value>taxon:41690</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>clone_lib</INSDQualifier_name>
          <INSDQualifier_value>venom duct cDNA library</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>country</INSDQualifier_name>
          <INSDQualifier_value>Panama</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>note</INSDQualifier_name>
          <INSDQualifier_value>isolated from the Bay of Panama</INSDQualifier_value>
        </INSDQualifier>
      </INSDFeature_quals>
    </INSDFeature>
    <INSDFeature>
      <INSDFeature_key>Protein</INSDFeature_key>
      <INSDFeature_location>&lt;1..67</INSDFeature_location>
      <INSDFeature_intervals>
        <INSDInterval>
          <INSDInterval_from>1</INSDInterval_from>
          <INSDInterval_to>67</INSDInterval_to>
          <INSDInterval_accession>AAQ05867.1</INSDInterval_accession>
        </INSDInterval>
      </INSDFeature_intervals>
      <INSDFeature_partial5 value="true"/>
      <INSDFeature_quals>
        <INSDQualifier>
          <INSDQualifier_name>product</INSDQualifier_name>
          <INSDQualifier_value>four-loop conotoxin preproprotein</INSDQualifier_value>
        </INSDQualifier>
      </INSDFeature_quals>
    </INSDFeature>
    <INSDFeature>
      <INSDFeature_key>mat_peptide</INSDFeature_key>
      <INSDFeature_location>41..67</INSDFeature_location>
      <INSDFeature_intervals>
        <INSDInterval>
          <INSDInterval_from>41</INSDInterval_from>
          <INSDInterval_to>67</INSDInterval_to>
          <INSDInterval_accession>AAQ05867.1</INSDInterval_accession>
        </INSDInterval>
      </INSDFeature_intervals>
      <INSDFeature_quals>
        <INSDQualifier>
          <INSDQualifier_name>product</INSDQualifier_name>
          <INSDQualifier_value>four-loop conotoxin</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>calculated_mol_wt</INSDQualifier_name>
          <INSDQualifier_value>3008</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>peptide</INSDQualifier_name>
          <INSDQualifier_value>PCKKTGRKCFPHQKDCCGRACIITICP</INSDQualifier_value>
        </INSDQualifier>
      </INSDFeature_quals>
    </INSDFeature>
    <INSDFeature>
      <INSDFeature_key>CDS</INSDFeature_key>
      <INSDFeature_location>1..67</INSDFeature_location>
      <INSDFeature_intervals>
        <INSDInterval>
          <INSDInterval_from>1</INSDInterval_from>
          <INSDInterval_to>67</INSDInterval_to>
          <INSDInterval_accession>AAQ05867.1</INSDInterval_accession>
        </INSDInterval>
      </INSDFeature_intervals>
      <INSDFeature_partial5 value="true"/>
      <INSDFeature_quals>
        <INSDQualifier>
          <INSDQualifier_name>coded_by</INSDQualifier_name>
          <INSDQualifier_value>AF480315.1:&lt;1..205</INSDQualifier_value>
        </INSDQualifier>
        <INSDQualifier>
          <INSDQualifier_name>codon_start</INSDQualifier_name>
          <INSDQualifier_value>2</INSDQualifier_value>
        </INSDQualifier>
      </INSDFeature_quals>
    </INSDFeature>
  </INSDSeq_feature-table>
  <INSDSeq_sequence>vvivavlfltacqlitaddsrrtqkhralrsttkratsnrpckktgrkcfphqkdccgraciiticp</INSDSeq_sequence>
</INSDSeq>
EOF
}

do_gene() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE DocumentSummary>
<DocumentSummary>
  <Id>3581</Id>
  <Name>IL9R</Name>
  <Description>interleukin 9 receptor</Description>
  <Status>0</Status>
  <CurrentID>0</CurrentID>
  <Chromosome>X, Y</Chromosome>
  <GeneticSource>genomic</GeneticSource>
  <MapLocation>Xq28 and Yq12</MapLocation>
  <OtherAliases>CD129, IL-9R</OtherAliases>
  <OtherDesignations>interleukin-9 receptor|IL-9 receptor</OtherDesignations>
  <NomenclatureSymbol>IL9R</NomenclatureSymbol>
  <NomenclatureName>interleukin 9 receptor</NomenclatureName>
  <NomenclatureStatus>Official</NomenclatureStatus>
  <Mim>
    <int>300007</int>
  </Mim>
  <GenomicInfo>
    <GenomicInfoType>
      <ChrLoc>X</ChrLoc>
      <ChrAccVer>NC_000023.11</ChrAccVer>
      <ChrStart>155997580</ChrStart>
      <ChrStop>156013016</ChrStop>
      <ExonCount>14</ExonCount>
    </GenomicInfoType>
    <GenomicInfoType>
      <ChrLoc>Y</ChrLoc>
      <ChrAccVer>NC_000024.10</ChrAccVer>
      <ChrStart>57184100</ChrStart>
      <ChrStop>57199536</ChrStop>
      <ExonCount>14</ExonCount>
    </GenomicInfoType>
  </GenomicInfo>
  <GeneWeight>5425</GeneWeight>
  <Summary>The protein encoded by this gene is a cytokine receptor that specifically mediates the biological effects of interleukin 9 (IL9).
The functional IL9 receptor complex requires this protein as well as the interleukin 2 receptor, gamma (IL2RG), a common gamma subunit shared by the receptors of many different cytokines.
The ligand binding of this receptor leads to the activation of various JAK kinases and STAT proteins, which connect to different biologic responses.
This gene is located at the pseudoautosomal regions of X and Y chromosomes.
Genetic studies suggested an association of this gene with the development of asthma.
Multiple pseudogenes on chromosome 9, 10, 16, and 18 have been described.
Alternatively spliced transcript variants have been found for this gene.</Summary>
  <ChrSort>X</ChrSort>
  <ChrStart>155997580</ChrStart>
  <Organism>
    <ScientificName>Homo sapiens</ScientificName>
    <CommonName>human</CommonName>
    <TaxID>9606</TaxID>
  </Organism>
</DocumentSummary>
EOF
}

do_taxon() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE TaxaSet>
<TaxaSet>
  <Taxon>
    <TaxId>9606</TaxId>
    <ScientificName>Homo sapiens</ScientificName>
    <OtherNames>
      <GenbankCommonName>human</GenbankCommonName>
      <CommonName>man</CommonName>
      <Name>
        <ClassCDE>authority</ClassCDE>
        <DispName>Homo sapiens Linnaeus, 1758</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Home sapiens</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sampiens</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapeins</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapian</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapians</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapien</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapience</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapiense</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapients</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo sapines</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo spaiens</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Homo spiens</DispName>
      </Name>
      <Name>
        <ClassCDE>misspelling</ClassCDE>
        <DispName>Humo sapiens</DispName>
      </Name>
    </OtherNames>
    <ParentTaxId>9605</ParentTaxId>
    <Rank>species</Rank>
    <Division>Primates</Division>
    <GeneticCode>
      <GCId>1</GCId>
      <GCName>Standard</GCName>
    </GeneticCode>
    <MitoGeneticCode>
      <MGCId>2</MGCId>
      <MGCName>Vertebrate Mitochondrial</MGCName>
    </MitoGeneticCode>
    <Lineage>cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo</Lineage>
    <LineageEx>
      <Taxon>
        <TaxId>131567</TaxId>
        <ScientificName>cellular organisms</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>2759</TaxId>
        <ScientificName>Eukaryota</ScientificName>
        <Rank>superkingdom</Rank>
      </Taxon>
      <Taxon>
        <TaxId>33154</TaxId>
        <ScientificName>Opisthokonta</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>33208</TaxId>
        <ScientificName>Metazoa</ScientificName>
        <Rank>kingdom</Rank>
      </Taxon>
      <Taxon>
        <TaxId>6072</TaxId>
        <ScientificName>Eumetazoa</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>33213</TaxId>
        <ScientificName>Bilateria</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>33511</TaxId>
        <ScientificName>Deuterostomia</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>7711</TaxId>
        <ScientificName>Chordata</ScientificName>
        <Rank>phylum</Rank>
      </Taxon>
      <Taxon>
        <TaxId>89593</TaxId>
        <ScientificName>Craniata</ScientificName>
        <Rank>subphylum</Rank>
      </Taxon>
      <Taxon>
        <TaxId>7742</TaxId>
        <ScientificName>Vertebrata</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>7776</TaxId>
        <ScientificName>Gnathostomata</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>117570</TaxId>
        <ScientificName>Teleostomi</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>117571</TaxId>
        <ScientificName>Euteleostomi</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>8287</TaxId>
        <ScientificName>Sarcopterygii</ScientificName>
        <Rank>superclass</Rank>
      </Taxon>
      <Taxon>
        <TaxId>1338369</TaxId>
        <ScientificName>Dipnotetrapodomorpha</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>32523</TaxId>
        <ScientificName>Tetrapoda</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>32524</TaxId>
        <ScientificName>Amniota</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>40674</TaxId>
        <ScientificName>Mammalia</ScientificName>
        <Rank>class</Rank>
      </Taxon>
      <Taxon>
        <TaxId>32525</TaxId>
        <ScientificName>Theria</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>9347</TaxId>
        <ScientificName>Eutheria</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>1437010</TaxId>
        <ScientificName>Boreoeutheria</ScientificName>
        <Rank>no rank</Rank>
      </Taxon>
      <Taxon>
        <TaxId>314146</TaxId>
        <ScientificName>Euarchontoglires</ScientificName>
        <Rank>superorder</Rank>
      </Taxon>
      <Taxon>
        <TaxId>9443</TaxId>
        <ScientificName>Primates</ScientificName>
        <Rank>order</Rank>
      </Taxon>
      <Taxon>
        <TaxId>376913</TaxId>
        <ScientificName>Haplorrhini</ScientificName>
        <Rank>suborder</Rank>
      </Taxon>
      <Taxon>
        <TaxId>314293</TaxId>
        <ScientificName>Simiiformes</ScientificName>
        <Rank>infraorder</Rank>
      </Taxon>
      <Taxon>
        <TaxId>9526</TaxId>
        <ScientificName>Catarrhini</ScientificName>
        <Rank>parvorder</Rank>
      </Taxon>
      <Taxon>
        <TaxId>314295</TaxId>
        <ScientificName>Hominoidea</ScientificName>
        <Rank>superfamily</Rank>
      </Taxon>
      <Taxon>
        <TaxId>9604</TaxId>
        <ScientificName>Hominidae</ScientificName>
        <Rank>family</Rank>
      </Taxon>
      <Taxon>
        <TaxId>207598</TaxId>
        <ScientificName>Homininae</ScientificName>
        <Rank>subfamily</Rank>
      </Taxon>
      <Taxon>
        <TaxId>9605</TaxId>
        <ScientificName>Homo</ScientificName>
        <Rank>genus</Rank>
      </Taxon>
    </LineageEx>
    <CreateDate>1995/02/27 09:24:00</CreateDate>
    <UpdateDate>2018/11/23 13:57:51</UpdateDate>
    <PubDate>1992/05/26 01:00:00</PubDate>
  </Taxon>
</TaxaSet>
EOF
}

do_blast() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE BlastOutput>
<BlastOutput>
  <BlastOutput_program>blastx</BlastOutput_program>
  <BlastOutput_version>BLASTX 2.2.29+</BlastOutput_version>
  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>nr</BlastOutput_db>
  <BlastOutput_query-ID>11471</BlastOutput_query-ID>
  <BlastOutput_query-def>Contig2</BlastOutput_query-def>
  <BlastOutput_query-len>620</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>3</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>L;</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_query-ID>11471</Iteration_query-ID>
      <Iteration_query-def>Contig2</Iteration_query-def>
      <Iteration_query-len>620</Iteration_query-len>
      <Iteration_hits>
        <Hit>
          <Hit_num>1</Hit_num>
          <Hit_id>gi|115476212|ref|NP_001061702.1|</Hit_id>
          <Hit_def>Os08g0384500 [Oryza sativa Japonica Group] &gt;gi|113623671|dbj|BAF23616.1| Os08g0384500, partial [Oryza sativa Japonica Group]</Hit_def>
          <Hit_accession>NP_001061702</Hit_accession>
          <Hit_len>763</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>357.066</Hsp_bit-score>
              <Hsp_score>915</Hsp_score>
              <Hsp_evalue>1.61032e-117</Hsp_evalue>
              <Hsp_query-from>8</Hsp_query-from>
              <Hsp_query-to>619</Hsp_query-to>
              <Hsp_hit-from>187</Hsp_hit-from>
              <Hsp_hit-to>390</Hsp_hit-to>
              <Hsp_query-frame>2</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>183</Hsp_identity>
              <Hsp_positive>195</Hsp_positive>
              <Hsp_gaps>0</Hsp_gaps>
              <Hsp_align-len>204</Hsp_align-len>
              <Hsp_qseq>DDRLLLLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGEIKISGYPKKQETFSRISGYCEQNDIHSPYVTLYESLLYSAWLRLPSDVNETQRKLFVEEVMNLVELSPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDXXXXXXXXXXXXNTVDTGRTVVCTIHQPSIDIFEAFDELFLI</Hsp_qseq>
              <Hsp_hseq>QDRLLLLKGVSGSFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGDISISGYPKKQETFARVSGYCEQNDIHSPNVTVYESLAYSAWLRLPSDVDSETRKMFIEQVMELVELNPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTVVCTIHQPSIDIFEAFDELFLM</Hsp_hseq>
              <Hsp_midline>DRLLLLKGVSG+FRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYI+G+I ISGYPKKQETF+R+SGYCEQNDIHSP VT+YESL YSAWLRLPSDV+ RK+F+E+VM LVEL+PLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMR VRNTVDTGRTVVCTIHQPSIDIFEAFDELFL+</Hsp_midline>
            </Hsp>
          </Hit_hsps>
        </Hit>
        <Hit>
          <Hit_num>2</Hit_num>
          <Hit_id>gi|218188640|gb|EEC71067.1|</Hit_id>
          <Hit_def>hypothetical protein OsI_02819 [Oryza sativa Indica Group]</Hit_def>
          <Hit_accession>EEC71067</Hit_accession>
          <Hit_len>517</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>344.354</Hsp_bit-score>
              <Hsp_score>882</Hsp_score>
              <Hsp_evalue>2.11484e-115</Hsp_evalue>
              <Hsp_query-from>8</Hsp_query-from>
              <Hsp_query-to>619</Hsp_query-to>
              <Hsp_hit-from>8</Hsp_hit-from>
              <Hsp_hit-to>211</Hsp_hit-to>
              <Hsp_query-frame>2</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>175</Hsp_identity>
              <Hsp_positive>197</Hsp_positive>
              <Hsp_gaps>0</Hsp_gaps>
              <Hsp_align-len>204</Hsp_align-len>
              <Hsp_qseq>DDRLLLLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGEIKISGYPKKQETFSRISGYCEQNDIHSPYVTLYESLLYSAWLRLPSDVNETQRKLFVEEVMNLVELSPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDXXXXXXXXXXXXNTVDTGRTVVCTIHQPSIDIFEAFDELFLI</Hsp_qseq>
              <Hsp_hseq>EERVLLLKGVSGSFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGDMRISGYPKKQETLARISGYCEQNDIHSPHVTVYESLVFSAWLRLPSEVDSEARKMFIEEVMDLVELTSLRGALVGLPGVSGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVNTGRTVVCTIHQPSIDIFEAFDELFLM</Hsp_hseq>
              <Hsp_midline>++R+LLLKGVSG+FRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYI+G+++ISGYPKKQET +RISGYCEQNDIHSP+VT+YESL++SAWLRLPS+V+ RK+F+EEVM+LVEL+ LR ALVGLPGV+GLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMR VRNTV+TGRTVVCTIHQPSIDIFEAFDELFL+</Hsp_midline>
            </Hsp>
          </Hit_hsps>
        </Hit>
        <Hit>
          <Hit_num>3</Hit_num>
          <Hit_id>gi|222640481|gb|EEE68613.1|</Hit_id>
          <Hit_def>hypothetical protein OsJ_27150 [Oryza sativa Japonica Group]</Hit_def>
          <Hit_accession>EEE68613</Hit_accession>
          <Hit_len>1199</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>357.066</Hsp_bit-score>
              <Hsp_score>915</Hsp_score>
              <Hsp_evalue>4.01633e-114</Hsp_evalue>
              <Hsp_query-from>8</Hsp_query-from>
              <Hsp_query-to>619</Hsp_query-to>
              <Hsp_hit-from>623</Hsp_hit-from>
              <Hsp_hit-to>826</Hsp_hit-to>
              <Hsp_query-frame>2</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>183</Hsp_identity>
              <Hsp_positive>195</Hsp_positive>
              <Hsp_gaps>0</Hsp_gaps>
              <Hsp_align-len>204</Hsp_align-len>
              <Hsp_qseq>DDRLLLLKGVSGAFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIDGEIKISGYPKKQETFSRISGYCEQNDIHSPYVTLYESLLYSAWLRLPSDVNETQRKLFVEEVMNLVELSPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDXXXXXXXXXXXXNTVDTGRTVVCTIHQPSIDIFEAFDELFLI</Hsp_qseq>
              <Hsp_hseq>QDRLLLLKGVSGSFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGDISISGYPKKQETFARVSGYCEQNDIHSPNVTVYESLAYSAWLRLPSDVDSETRKMFIEQVMELVELNPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTVVCTIHQPSIDIFEAFDELFLM</Hsp_hseq>
              <Hsp_midline>DRLLLLKGVSG+FRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYI+G+I ISGYPKKQETF+R+SGYCEQNDIHSP VT+YESL YSAWLRLPSDV+ RK+F+E+VM LVEL+PLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMR VRNTVDTGRTVVCTIHQPSIDIFEAFDELFL+</Hsp_midline>
            </Hsp>
            <Hsp>
              <Hsp_num>2</Hsp_num>
              <Hsp_bit-score>44.669</Hsp_bit-score>
              <Hsp_score>104</Hsp_score>
              <Hsp_evalue>0.00011956</Hsp_evalue>
              <Hsp_query-from>293</Hsp_query-from>
              <Hsp_query-to>619</Hsp_query-to>
              <Hsp_hit-from>49</Hsp_hit-from>
              <Hsp_hit-to>158</Hsp_hit-to>
              <Hsp_query-frame>2</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>30</Hsp_identity>
              <Hsp_positive>58</Hsp_positive>
              <Hsp_gaps>1</Hsp_gaps>
              <Hsp_align-len>110</Hsp_align-len>
              <Hsp_qseq>DVNETQRKLFVEEVMNLVELSPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDXXXXXXXXXXXXN-TVDTGRTVVCTIHQPSIDIFEAFDELFLI</Hsp_qseq>
              <Hsp_hseq>SVGGQETNIITDYVLKILGLDICADTIVGNEMLRGISGGQRKRVTTGEMIVGPARAMFMDEISTGLDSSTTFQIVKSLGQITSILGGTTVISLLQPAPETYNLFDDIILL</Hsp_hseq>
              <Hsp_midline>V + + + V+ ++ L D +VG + G+S QRKR+T +V +FMDE ++GLD+ +++++ T G T V ++ QP+ + + FD++ L+</Hsp_midline>
            </Hsp>
          </Hit_hsps>
        </Hit>
      </Iteration_hits>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>160101</Statistics_db-num>
          <Statistics_db-len>61990885</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.041</Statistics_kappa>
          <Statistics_lambda>0.267</Statistics_lambda>
          <Statistics_entropy>0.14</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
    </Iteration>
  </BlastOutput_iterations>
</BlastOutput>
EOF
}

do_snp() {
  cat <<EOF
{
  "refsnp_id": "1238141906",
  "create_date": "2017-11-9T09:55Z",
  "last_update_date": "2018-10-13T04:05Z",
  "last_update_build_id": "152",
  "dbsnp1_merges": [],
  "citations": [],
  "lost_obs_movements": [],
  "present_obs_movements": [
    {
      "component_ids": [
        {
          "type": "subsnp",
          "value": "3625249109"
        }
      ],
      "observation": {
        "seq_id": "NC_000023.11",
        "position": 154187777,
        "deleted_sequence": "G",
        "inserted_sequence": "G"
      },
      "allele_in_cur_release": {
        "seq_id": "NC_000023.11",
        "position": 154187777,
        "deleted_sequence": "G",
        "inserted_sequence": "G"
      },
      "other_rsids_in_cur_release": [],
      "previous_release": {
        "allele": {
          "seq_id": "NC_000023.11",
          "position": 154187777,
          "deleted_sequence": "G",
          "inserted_sequence": "G"
        },
        "rsids": [
          "1238141906"
        ]
      },
      "last_added_to_this_rs": "151"
    },
    {
      "component_ids": [
        {
          "type": "subsnp",
          "value": "3625249109"
        }
      ],
      "observation": {
        "seq_id": "NC_000023.11",
        "position": 154187777,
        "deleted_sequence": "G",
        "inserted_sequence": "A"
      },
      "allele_in_cur_release": {
        "seq_id": "NC_000023.11",
        "position": 154187777,
        "deleted_sequence": "G",
        "inserted_sequence": "A"
      },
      "other_rsids_in_cur_release": [],
      "previous_release": {
        "allele": {
          "seq_id": "NC_000023.11",
          "position": 154187777,
          "deleted_sequence": "G",
          "inserted_sequence": "A"
        },
        "rsids": [
          "1238141906"
        ]
      },
      "last_added_to_this_rs": "151"
    }
  ],
  "primary_snapshot_data": {
    "placements_with_allele": [
      {
        "seq_id": "NC_000023.11",
        "is_ptlp": true,
        "placement_annot": {
          "seq_type": "refseq_chromosome",
          "mol_type": "genomic",
          "seq_id_traits_by_assembly": [
            {
              "assembly_name": "GRCh38.p12",
              "assembly_accession": "GCF_000001405.38",
              "is_top_level": true,
              "is_alt": false,
              "is_patch": false,
              "is_chromosome": true
            }
          ],
          "is_aln_opposite_orientation": false,
          "is_mismatch": false
        },
        "alleles": [
          {
            "allele": {
              "spdi": {
                "seq_id": "NC_000023.11",
                "position": 154187777,
                "deleted_sequence": "G",
                "inserted_sequence": "G"
              }
            },
            "hgvs": "NC_000023.11:g.154187778G="
          },
          {
            "allele": {
              "spdi": {
                "seq_id": "NC_000023.11",
                "position": 154187777,
                "deleted_sequence": "G",
                "inserted_sequence": "A"
              }
            },
            "hgvs": "NC_000023.11:g.154187778G>A"
          }
        ]
      },
      {
        "seq_id": "NW_003871103.3",
        "is_ptlp": false,
        "placement_annot": {
          "seq_type": "refseq_chromosome",
          "mol_type": "genomic",
          "seq_id_traits_by_assembly": [
            {
              "assembly_name": "GRCh37.p13",
              "assembly_accession": "GCF_000001405.25",
              "is_top_level": true,
              "is_alt": false,
              "is_patch": true,
              "is_chromosome": false
            }
          ],
          "is_aln_opposite_orientation": false,
          "is_mismatch": false
        },
        "alleles": [
          {
            "allele": {
              "spdi": {
                "seq_id": "NW_003871103.3",
                "position": 1621756,
                "deleted_sequence": "G",
                "inserted_sequence": "G"
              }
            },
            "hgvs": "NW_003871103.3:g.1621757G="
          },
          {
            "allele": {
              "spdi": {
                "seq_id": "NW_003871103.3",
                "position": 1621756,
                "deleted_sequence": "G",
                "inserted_sequence": "A"
              }
            },
            "hgvs": "NW_003871103.3:g.1621757G>A"
          }
        ]
      },
      {
        "seq_id": "NG_011606.1",
        "is_ptlp": false,
        "placement_annot": {
          "seq_type": "refseq_genomic",
          "mol_type": "genomic",
          "seq_id_traits_by_assembly": [],
          "is_aln_opposite_orientation": false,
          "is_mismatch": false
        },
        "alleles": [
          {
            "allele": {
              "spdi": {
                "seq_id": "NG_011606.1",
                "position": 10182,
                "deleted_sequence": "G",
                "inserted_sequence": "G"
              }
            },
            "hgvs": "NG_011606.1:g.10183G="
          },
          {
            "allele": {
              "spdi": {
                "seq_id": "NG_011606.1",
                "position": 10182,
                "deleted_sequence": "G",
                "inserted_sequence": "A"
              }
            },
            "hgvs": "NG_011606.1:g.10183G>A"
          }
        ]
      },
      {
        "seq_id": "NM_000513.2",
        "is_ptlp": false,
        "placement_annot": {
          "seq_type": "refseq_mrna",
          "mol_type": "rna",
          "seq_id_traits_by_assembly": [],
          "is_aln_opposite_orientation": false,
          "is_mismatch": false
        },
        "alleles": [
          {
            "allele": {
              "spdi": {
                "seq_id": "NM_000513.2",
                "position": 202,
                "deleted_sequence": "G",
                "inserted_sequence": "G"
              }
            },
            "hgvs": "NM_000513.2:c.121G="
          },
          {
            "allele": {
              "spdi": {
                "seq_id": "NM_000513.2",
                "position": 202,
                "deleted_sequence": "G",
                "inserted_sequence": "A"
              }
            },
            "hgvs": "NM_000513.2:c.121G>A"
          }
        ]
      },
      {
        "seq_id": "NC_000023.10",
        "is_ptlp": false,
        "placement_annot": {
          "seq_type": "refseq_chromosome",
          "mol_type": "genomic",
          "seq_id_traits_by_assembly": [
            {
              "assembly_name": "GRCh37.p13",
              "assembly_accession": "GCF_000001405.25",
              "is_top_level": true,
              "is_alt": false,
              "is_patch": false,
              "is_chromosome": true
            }
          ],
          "is_aln_opposite_orientation": false,
          "is_mismatch": false
        },
        "alleles": [
          {
            "allele": {
              "spdi": {
                "seq_id": "NC_000023.10",
                "position": 153453266,
                "deleted_sequence": "G",
                "inserted_sequence": "G"
              }
            },
            "hgvs": "NC_000023.10:g.153453267G="
          },
          {
            "allele": {
              "spdi": {
                "seq_id": "NC_000023.10",
                "position": 153453266,
                "deleted_sequence": "G",
                "inserted_sequence": "A"
              }
            },
            "hgvs": "NC_000023.10:g.153453267G>A"
          }
        ]
      },
      {
        "seq_id": "NP_000504.1",
        "is_ptlp": false,
        "placement_annot": {
          "seq_type": "refseq_prot",
          "mol_type": "protein",
          "seq_id_traits_by_assembly": [],
          "is_aln_opposite_orientation": false,
          "is_mismatch": false
        },
        "alleles": [
          {
            "allele": {
              "spdi": {
                "seq_id": "NP_000504.1",
                "position": 40,
                "deleted_sequence": "E",
                "inserted_sequence": "E"
              }
            },
            "hgvs": "NP_000504.1:p.Glu41="
          },
          {
            "allele": {
              "spdi": {
                "seq_id": "NP_000504.1",
                "position": 40,
                "deleted_sequence": "E",
                "inserted_sequence": "K"
              }
            },
            "hgvs": "NP_000504.1:p.Glu41Lys"
          }
        ]
      }
    ],
    "allele_annotations": [
      {
        "frequency": [],
        "clinical": [],
        "submissions": [
          "3625249109"
        ],
        "assembly_annotation": [
          {
            "seq_id": "NC_000023.11",
            "annotation_release": "Homo sapiens Annotation Release 109",
            "genes": [
              {
                "name": "opsin 1, medium wave sensitive",
                "id": 2652,
                "locus": "OPN1MW",
                "is_pseudo": false,
                "orientation": "plus",
                "sequence_ontology": [],
                "rnas": [
                  {
                    "id": "NM_000513.2",
                    "codon_aligned_transcript_change": {
                      "seq_id": "NM_000513.2",
                      "position": 202,
                      "deleted_sequence": "GAA",
                      "inserted_sequence": "GAA"
                    },
                    "sequence_ontology": [
                      {
                        "name": "coding_sequence_variant",
                        "accession": "SO:0001580"
                      }
                    ],
                    "product_id": "NP_000504.1",
                    "protein": {
                      "variant": {
                        "spdi": {
                          "seq_id": "NP_000504.1",
                          "position": 40,
                          "deleted_sequence": "E",
                          "inserted_sequence": "E"
                        }
                      },
                      "sequence_ontology": []
                    }
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "frequency": [],
        "clinical": [],
        "submissions": [
          "3625249109"
        ],
        "assembly_annotation": [
          {
            "seq_id": "NC_000023.11",
            "annotation_release": "Homo sapiens Annotation Release 109",
            "genes": [
              {
                "name": "opsin 1, medium wave sensitive",
                "id": 2652,
                "locus": "OPN1MW",
                "is_pseudo": false,
                "orientation": "plus",
                "sequence_ontology": [],
                "rnas": [
                  {
                    "id": "NM_000513.2",
                    "codon_aligned_transcript_change": {
                      "seq_id": "NM_000513.2",
                      "position": 202,
                      "deleted_sequence": "GAA",
                      "inserted_sequence": "AAA"
                    },
                    "sequence_ontology": [
                      {
                        "name": "coding_sequence_variant",
                        "accession": "SO:0001580"
                      }
                    ],
                    "product_id": "NP_000504.1",
                    "protein": {
                      "variant": {
                        "spdi": {
                          "seq_id": "NP_000504.1",
                          "position": 40,
                          "deleted_sequence": "E",
                          "inserted_sequence": "K"
                        }
                      },
                      "sequence_ontology": [
                        {
                          "name": "missense_variant",
                          "accession": "SO:0001583"
                        }
                      ]
                    }
                  }
                ]
              }
            ]
          }
        ]
      }
    ],
    "support": [
      {
        "id": {
          "type": "subsnp",
          "value": "ss3625249109"
        },
        "revision_added": "151",
        "create_date": "2017-11-8T14:58Z",
        "submitter_handle": "TOPMED"
      }
    ],
    "anchor": "NC_000023.11:0154187777:1:snv",
    "variant_type": "snv"
  }
}
EOF
}

do_bioc() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE collection>
<collection>
  <source>PubMed</source>
  <date>20171216</date>
  <key>collection.key</key>
  <document>
    <id>6301692</id>
    <passage>
      <infon key="type">title</infon>
      <offset>0</offset>
      <text>Site-specific relaxation and recombination by the Tn3 resolvase: recognition of the DNA path between oriented res sites.</text>
    </passage>
    <passage>
      <infon key="type">abstract</infon>
      <offset>121</offset>
      <text>We studied the dynamics of site-specific recombination by the resolvase encoded by the Escherichia coli transposon Tn3. The pure enzyme recombined supercoiled plasmids containing two directly repeated recombination sites, called res sites. Resolvase is the first strictly site-specific topoisomerase. It relaxed only plasmids containing directly repeated res sites; substrates with zero, one or two inverted sites were inert. Even when the proximity of res sites was ensured by catenation of plasmids with a single site, neither relaxation nor recombination occurred. The two circular products of recombination were catenanes interlinked only once. These properties of resolvase require that the path of the DNA between res sites be clearly defined and that strand exchange occur with a unique geometry. A model in which one subunit of a dimeric resolvase is bound at one res site, while the other searches along adjacent DNA until it encounters the second site, would account for the ability of resolvase to distinguish intramolecular from intermolecular sites, to sense the relative orientation of sites and to produce singly interlinked catenanes. Because resolvase is a type 1 topoisomerase, we infer that it makes the required duplex bDNA breaks of recombination one strand at a time.</text>
    </passage>
  </document>
</collection>
EOF
}

do_flatfile() {
  cat <<EOF
LOCUS       DMU54469                2881 bp    DNA     linear   INV 20-JUN-2017
DEFINITION  Drosophila melanogaster eukaryotic initiation factor 4E (eIF4E)
            gene, complete cds, alternatively spliced.
ACCESSION   U54469
VERSION     U54469.1  GI:1322283
KEYWORDS    .
SOURCE      Drosophila melanogaster (fruit fly)
  ORGANISM  Drosophila melanogaster
            Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
            Pterygota; Neoptera; Holometabola; Diptera; Brachycera;
            Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora.
REFERENCE   1  (bases 1 to 2881)
  AUTHORS   Lavoie,C.A., Lachance,P.E., Sonenberg,N. and Lasko,P.
  TITLE     Alternatively spliced transcripts from the Drosophila eIF4E gene
            produce two different Cap-binding proteins
  JOURNAL   J. Biol. Chem. 271 (27), 16393-16398 (1996)
   PUBMED   8663200
REFERENCE   2  (bases 1 to 2881)
  AUTHORS   Lasko,P.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-1996) Paul F. Lasko, Biology, McGill University,
            1205 Avenue Docteur Penfield, Montreal, QC H3A 1B1, Canada
FEATURES             Location/Qualifiers
     source          1..2881
                     /organism="Drosophila melanogaster"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:7227"
                     /chromosome="3"
                     /map="67A8-B2"
     gene            80..2881
                     /gene="eIF4E"
     mRNA            join(80..224,892..1458,1550..1920,1986..2085,2317..2404,
                     2466..2881)
                     /gene="eIF4E"
                     /product="eukaryotic initiation factor 4E-I"
     mRNA            join(80..224,1550..1920,1986..2085,2317..2404,2466..2881)
                     /gene="eIF4E"
                     /product="eukaryotic initiation factor 4E-II"
     CDS             join(201..224,1550..1920,1986..2085,2317..2404,2466..2629)
                     /gene="eIF4E"
                     /note="Method: conceptual translation with partial peptide
                     sequencing"
                     /codon_start=1
                     /product="eukaryotic initiation factor 4E-II"
                     /protein_id="AAC03524.1"
                     /db_xref="GI:1322284"
                     /translation="MVVLETEKTSAPSTEQGRPEPPTSAAAPAEAKDVKPKEDPQETG
                     EPAGNTATTTAPAGDDAVRTEHLYKHPLMNVWTLWYLENDRSKSWEDMQNEITSFDTV
                     EDFWSLYNHIKPPSEIKLGSDYSLFKKNIRPMWEDAANKQGGRWVITLNKSSKTDLDN
                     LWLDVLLCLIGEAFDHSDQICGAVINIRGKSNKISIWTADGNNEEAALEIGHKLRDAL
                     RLGRNNSLQYQLHKDTMVKQGSNVKSIYTL"
     CDS             join(1402..1458,1550..1920,1986..2085,2317..2404,
                     2466..2629)
                     /gene="eIF4E"
                     /note="Method: conceptual translation with partial peptide
                     sequencing; two alternatively spliced transcripts both
                     encode 4E-I"
                     /codon_start=1
                     /product="eukaryotic initiation factor 4E-I"
                     /protein_id="AAC03525.1"
                     /db_xref="GI:1322285"
                     /translation="MQSDFHRMKNFANPKSMFKTSAPSTEQGRPEPPTSAAAPAEAKD
                     VKPKEDPQETGEPAGNTATTTAPAGDDAVRTEHLYKHPLMNVWTLWYLENDRSKSWED
                     MQNEITSFDTVEDFWSLYNHIKPPSEIKLGSDYSLFKKNIRPMWEDAANKQGGRWVIT
                     LNKSSKTDLDNLWLDVLLCLIGEAFDHSDQICGAVINIRGKSNKISIWTADGNNEEAA
                     LEIGHKLRDALRLGRNNSLQYQLHKDTMVKQGSNVKSIYTL"
BASE COUNT      849 a    699 c    585 g    748 t
ORIGIN
        1 cggttgcttg ggttttataa catcagtcag tgacaggcat ttccagagtt gccctgttca
       61 acaatcgata gctgcctttg gccaccaaaa tcccaaactt aattaaagaa ttaaataatt
      121 cgaataataa ttaagcccag taacctacgc agcttgagtg cgtaaccgat atctagtata
      181 catttcgata catcgaaatc atggtagtgt tggagacgga gaaggtaaga cgatgataga
      241 cggcgagccg catgggttcg atttgcgctg agccgtggca gggaacaaca aaaacagggt
      301 tgttgcacaa gaggggaggc gatagtcgag cggaaaagag tgcagttggc gtggctacat
      361 catcattgtg ttcaccgatt attttttgca caattgctta atattaattg tacttgcacg
      421 ctattgtcta cgtcatagct atcgctcatc tctgtctgtc tctatcaagc tatctctctt
      481 tcgcggtcac tcgttctctt ttttctctcc tttcgcattt gcatacgcat accacacgtt
      541 ttcagtgttc tcgctctctc tctcttgtca agacatcgcg cgcgtgtgtg tgggtgtgtc
      601 tctagcacat atacataaat aggagagcgg agagacaaat atggaaagaa tgaaaaagag
      661 tgaattactg caattaacca gtcgcgaaca gttaaatcat atttttgtcg gccattgcag
      721 taaataaacc gttggctttc cctccttcac tttccacctc ctttcttgac gttaattttt
      781 tcagttaatc gcgccgctgc tttgaactcg aacacgaatt ttagccgcaa cataaaataa
      841 aatcaagtaa ctctttaact caatataaaa caacaatcca atcttcaaca ggcaatctgt
      901 gtttttatgt cagatacgag cgcgtgtgtg tgtgtgctgt aattccatcg cccctttcga
      961 ttccgagttc gttaggaaca gcattagttc gcctatttta gtagtagcct agtccgattt
     1021 taagtgaaac aggacactcc aacaccatat acgcaataat tagttaccac ccactcaacc
     1081 atacagcaac aacaagttta acgagttttt tgtattatca ttacttagtt ttttggttaa
     1141 taatacaaca agtgaagagc gaactgcagg ggagcgagga tatcacgaaa caatccaaaa
     1201 tccacacaca ctcaaacaga aatcaaaagc ttcgctctct cgcacacaca cgcaccaacc
     1261 aactatcaac tatcacaaac accgcgacag agagagagcg gcaagtgaat cacggcgaat
     1321 cgaaaccgat ccgaacccac tccggagccg aaaaagaact gatcctacca tcaaacgcat
     1381 ccaataaaca cggccgccaa catgcagagc gactttcaca gaatgaagaa ctttgccaat
     1441 cccaagtcca tgttcaaagt aatactctca gtgcgcctgt cgctaagcca agccaagcta
     1501 atctaatctt ctgattcccc ttcccatcca ttgccatctt ctcccgcaga ccagcgcccc
     1561 cagcaccgag cagggtcgtc cggaaccacc aacttcggct gcagcgcccg ccgaggctaa
     1621 ggatgtcaag cccaaggagg acccacagga gactggtgaa ccagcaggca acactgcaac
     1681 cactactgct cctgccggcg acgatgctgt gcgcaccgag catttataca aacacccgct
     1741 catgaatgtc tggacgctgt ggtaccttga aaacgatcgg tccaagtcct gggaggacat
     1801 gcaaaacgag atcaccagct tcgataccgt cgaggacttc tggagcctat acaaccacat
     1861 caagccccca tcagagatca agctgggtag tgactactcg ctattcaaga agaacattcg
     1921 gtgggtttgc tgttttattg caatttctac caagataacc tttactaact gatatctcat
     1981 tgcagtccca tgtgggagga tgcagccaac aaacagggcg gtcgttgggt cattaccctt
     2041 aacaaaagct ccaagaccga tctggataac ctatggctcg atgtggtaag tgcacaaaga
     2101 acgagtggtt agaggatgtc tattatagtg aatgtacatt cttgaaatgc aaaaatatag
     2161 aaataggtgt atgattttgc agtataaatt ataacttata gaaaatatca gctaaaaata
     2221 cgctagtgtt agcttttgtc ttaggaacat tcaatagtga gcttatatca taaatatctt
     2281 tcgcatatga gtaactacaa ctgttttgcc ttccagctgc tctgcctgat tggcgaggcc
     2341 ttcgatcact ccgatcagat ctgcggcgct gttataaaca ttcgcggcaa gagcaacaag
     2401 atatgtaagt tttcacgcac acccaacttc agcggaattc ctttgtttaa cattaatctt
     2461 tccagccatc tggactgccg acggaaacaa cgaggaagct gcccttgaga ttggtcacaa
     2521 gctgcgcgat gccttgcgtc tgggacgcaa caactcgctg cagtatcagt tgcacaagga
     2581 cacgatggtc aagcagggct ccaacgtgaa atcgatctac actttgtagg cggctaataa
     2641 ctggccgctc cttactcggt ccgatcccac acagattagt ttgtctttca tttatttatc
     2701 gttataagca acagtagcga ttaatcgtga ctattgtcta agacccgcgt aacgaaaccg
     2761 aaacggaacc ccctttgtta tcaaaaatcg gcataatata aaatctatcc gctttttgta
     2821 gtcactgtca ataatggatt agacggaaaa gtatattaat aaaaacctac attaaaaccg
     2881 g
//
LOCUS       AAC03524                 248 aa            linear   INV 20-JUN-2017
DEFINITION  eukaryotic initiation factor 4E-II [Drosophila melanogaster].
ACCESSION   AAC03524
VERSION     AAC03524.1  GI:1322284
DBSOURCE    locus DMU54469 accession U54469.1
KEYWORDS    .
SOURCE      Drosophila melanogaster (fruit fly)
  ORGANISM  Drosophila melanogaster
            Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
            Pterygota; Neoptera; Holometabola; Diptera; Brachycera;
            Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora.
REFERENCE   1  (residues 1 to 248)
  AUTHORS   Lavoie,C.A., Lachance,P.E., Sonenberg,N. and Lasko,P.
  TITLE     Alternatively spliced transcripts from the Drosophila eIF4E gene
            produce two different Cap-binding proteins
  JOURNAL   J. Biol. Chem. 271 (27), 16393-16398 (1996)
   PUBMED   8663200
REFERENCE   2  (residues 1 to 248)
  AUTHORS   Lasko,P.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-1996) Paul F. Lasko, Biology, McGill University,
            1205 Avenue Docteur Penfield, Montreal, QC H3A 1B1, Canada
COMMENT     Method: conceptual translation with partial peptide sequencing.
FEATURES             Location/Qualifiers
     source          1..248
                     /organism="Drosophila melanogaster"
                     /db_xref="taxon:7227"
                     /chromosome="3"
                     /map="67A8-B2"
     Protein         1..248
                     /product="eukaryotic initiation factor 4E-II"
     CDS             1..248
                     /gene="eIF4E"
                     /coded_by="join(U54469.1:201..224,U54469.1:1550..1920,
                     U54469.1:1986..2085,U54469.1:2317..2404,
                     U54469.1:2466..2629)"
ORIGIN
        1 mvvletekts apsteqgrpe pptsaaapae akdvkpkedp qetgepagnt atttapagdd
       61 avrtehlykh plmnvwtlwy lendrskswe dmqneitsfd tvedfwslyn hikppseikl
      121 gsdyslfkkn irpmwedaan kqggrwvitl nkssktdldn lwldvllcli geafdhsdqi
      181 cgavinirgk snkisiwtad gnneeaalei ghklrdalrl grnnslqyql hkdtmvkqgs
      241 nvksiytl
//
EOF
}

do_gencode() {
  cat <<EOF

Standard Genetic Code Table

                           Second Position
  First      T             C             A             G      Third
  -----------------------------------------------------------------
    T   TTT Phe [F]   TCT Ser [S]   TAT Tyr [Y]   TGT Cys [C]   T
        TTC Phe [F]   TCC Ser [S]   TAC Tyr [Y]   TGC Cys [C]   C
        TTA Leu [L]   TCA Ser [S]   TAA Och [*]   TGA Opa [*]   A
        TTG Leu [L]   TCG Ser [S]   TAG Amb [*]   TGG Trp [W]   G
  -----------------------------------------------------------------
    C   CTT Leu [L]   CCT Pro [P]   CAT His [H]   CGT Arg [R]   T
        CTC Leu [L]   CCC Pro [P]   CAC His [H]   CGC Arg [R]   C
        CTA Leu [L]   CCA Pro [P]   CAA Gln [Q]   CGA Arg [R]   A
        CTG Leu [L]   CCG Pro [P]   CAG Gln [Q]   CGG Arg [R]   G
  -----------------------------------------------------------------
    A   ATT Ile [I]   ACT Thr [T]   AAT Asn [N]   AGT Ser [S]   T
        ATC Ile [I]   ACC Thr [T]   AAC Asn [N]   AGC Ser [S]   C
        ATA Ile [I]   ACA Thr [T]   AAA Lys [K]   AGA Arg [R]   A
        ATG Met [M]   ACG Thr [T]   AAG Lys [K]   AGG Arg [R]   G
  -----------------------------------------------------------------
    G   GTT Val [V]   GCT Ala [A]   GAT Asp [D]   GGT Gly [G]   T
        GTC Val [V]   GCC Ala [A]   GAC Asp [D]   GGC Gly [G]   C
        GTA Val [V]   GCA Ala [A]   GAA Glu [E]   GGA Gly [G]   A
        GTG Val [V]   GCG Ala [A]   GAG Glu [E]   GGG Gly [G]   G
  -----------------------------------------------------------------

Amino Acid Abbreviations

  Alanine          Ala   A                  |   A   Ala   Alanine
  Arginine         Arg   R   R-ginine       |   B   Asx   Asp or Asn
  Asparagine       Asn   N   asparagiNe     |   C   Cys   Cysteine
  Aspartic Acid    Asp   D   asparDic       |   D   Asp   Aspartic Acid
  Cysteine         Cys   C                  |   E   Glu   Glutamic Acid
  Glutamic Acid    Glu   E   gluE           |   F   Phe   Phenylalanine
  Glutamine        Gln   Q   Q-tamine       |   G   Gly   Glycine
  Glycine          Gly   G                  |   H   His   Histidine
  Histidine        His   H                  |   I   Ile   Isoleucine
  Isoleucine       Ile   I                  |   J   Xle   Leu or Ile
  Leucine          Leu   L                  |   K   Lys   Lysine
  Lysine           Lys   K   next to L      |   L   Leu   Leucine
  Methionine       Met   M                  |   M   Met   Methionine
  Phenylalanine    Phe   F   Fenylalanine   |   N   Asn   Asparagine
  Proline          Pro   P                  |   O   Pyl   Pyrrolysine
  Pyrrolysine      Pyl   O   pyrrOlysine    |   P   Pro   Proline
  Selenocysteine   Sec   U                  |   Q   Gln   Glutamine
  Serine           Ser   S                  |   R   Arg   Arginine
  Threonine        Thr   T                  |   S   Ser   Serine
  Tryptophan       Trp   W   tWyptophan     |   T   Thr   Threonine
  Tyrosine         Tyr   Y   tYrosine       |   U   Sec   Selenocysteine
  Valine           Val   V                  |   V   Val   Valine
  Asp or Asn       Asx   B                  |   W   Trp   Tryptophan
  Glu or Gln       Glx   Z                  |   X   Xxx   Undetermined
  Leu or Ile       Xle   J                  |   Y   Tyr   Tyrosine
  Undetermined     Xxx   X                  |   Z   Glx   Glu or Gln
  Termination      Ter   *                  |   *   Ter   Termination

  -----------------------------------------------------------------

Nucleotide Abbreviations

            R   AG   puRine       |   H   ACT    not G
            Y   CT   pYrimidine   |   B   CGT    not A
            M   AC   aMino        |   V   ACG    not T
            K   GT   Keto         |   D   AGT    not C
            S   CG   Strong       |   N   ACGT   unkNown
            W   AT   Weak         |   X   ACGT   unknown

Genetic Code Names

  1:     Standard
  2:     Vertebrate Mitochondrial
  3:     Yeast Mitochondrial
  4:     Mold Mitochondrial; Protozoan Mitochondrial;
         Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
  5:     Invertebrate Mitochondrial
  6:     Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
  9:     Echinoderm Mitochondrial; Flatworm Mitochondrial
  10:    Euplotid Nuclear
  11:    Bacterial, Archaeal and Plant Plastid
  12:    Alternative Yeast Nuclear
  13:    Ascidian Mitochondrial
  14:    Alternative Flatworm Mitochondrial
  15:    Blepharisma Macronuclear
  16:    Chlorophycean Mitochondrial
  21:    Trematode Mitochondrial
  22:    Scenedesmus obliquus Mitochondrial
  23:    Thraustochytrium Mitochondrial
  24:    Rhabdopleuridae Mitochondrial
  25:    Candidate Division SR1 and Gracilibacteria
  26:    Pachysolen tannophilus Nuclear
  27:    Karyorelict Nuclear
  28:    Condylostoma Nuclear
  29:    Mesodinium Nuclear
  30:    Peritrich Nuclear
  31:    Blastocrithidia Nuclear
  32:    Balanophoraceae Plastid
  33:    Cephalodiscidae Mitochondrial

EOF
}

do_error() {
  cat <<EOF
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE eInfoResult>
<eInfoResult>
  <ERROR>Can not retrieve DbInfo for db=all</ERROR>
</eInfoResult>
EOF
}

choice="help"

if [ $# -gt 0 ]
then
  choice="$1"
fi

case "$choice" in
    help | -help )
     do_help 
     ;;
    docsum | -docsum )
     do_docsum 
     ;;
    article | -article | pubmed | -pubmed )
     do_article 
     ;;
    book | -book )
     do_book 
     ;;
    protein | -protein )
     do_protein 
     ;;
    gene | -gene )
     do_gene 
     ;;
    taxon | -taxon )
     do_taxon 
     ;;
    blast | -blast )
     do_blast 
     ;;
    snp | -snp )
     do_snp 
     ;;
    bioc | -bioc )
     do_bioc 
     ;;
    flatfile | -flatfile )
     do_flatfile 
     ;;
    gencode | -gencode )
     do_gencode 
     ;;
    error | -error )
     do_error 
     ;;
esac