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Source: ruby-crb-blast
Maintainer: Debian Ruby Extras Maintainers <pkg-ruby-extras-maintainers@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
Section: ruby
Testsuite: autopkgtest-pkg-ruby
Priority: optional
Build-Depends: debhelper-compat (= 12),
gem2deb,
help2man,
ncbi-blast+,
rake,
ruby-bio,
ruby-fixwhich,
ruby-shoulda,
ruby-threach,
ruby-trollop
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/ruby-team/ruby-crb-blast
Vcs-Git: https://salsa.debian.org/ruby-team/ruby-crb-blast.git
Homepage: https://github.com/cboursnell/crb-blast
XS-Ruby-Versions: all
Rules-Requires-Root: no
Package: ruby-crb-blast
Architecture: all
Depends: ncbi-blast+,
ruby | ruby-interpreter,
ruby-bio,
ruby-fixwhich,
ruby-threach,
ruby-trollop,
${misc:Depends}
Description: Run conditional reciprocal best blast
CRB-BLAST is a novel method for finding orthologs between one set of sequences
and another. This is particularly useful in genome and transcriptome
annotation.
.
CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by
performing BLAST alignments of query->target and target->query. Reciprocal
best BLAST hits are those where the best match for any given query sequence in
the query->target alignment is also the best hit of the match in the reverse
(target->query) alignment.
.
Reciprocal best BLAST is a very conservative way to assign orthologs. The main
innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to
each pairwise alignment by taking into account the overall relatedness of the
two datasets being compared. This is done by fitting a function to the
distribution of alignment e-values over sequence lengths. The function
provides the e-value cutoff for a sequence of given length.
XB-Ruby-Versions: ${ruby:Versions}
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