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Enhancements:
A new option has been added to search multiple queries at once for the
blastn and tblastn program options of blastall.
-B Number of concatenated queries, for blastn and tblastn [Integer]
Optional
default = 0
This new feature similar in principle, but different in implementation
from the support for multiple queries already existing in megablast.
The combination of ungapped search (-g F) and multiple queries
(-B N) is not supported. The argument to -B option must be equal
to the number of sequences in the FASTA input file.
Processing multiple query sequences in one run can be much faster than
processing them with separate runs because the database is scanned only 1
time for the entire set of queries. When the -B option is used, the
results may differ from the ones produced with individual queries. Usually
results will be at least as good or better (in terms of score/evalue)
than the results of corresponding individual queries; exceptions occur
due to the heuristic nature of BLAST. Additional alignments may appear.
It is guaranteed that matching sequences will
appear in the same order when they are tied in evalue
and are part of the output both with and without -B.
When the -B option is used, the summary statistics at the bottom
of the output are for the combined set of queries; at present,
the summary statistics are not tabulated for the individual
queries in a multiple-query input.
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