Paket: ruby-crb-blast (0.6.9-5)

[ Källkod: ruby-crb-blast  ]

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.

Andra paket besläktade med ruby-crb-blast

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: ruby

  Interpreter of object-oriented scripting language Ruby (default version)

• dep: ruby-bio (>= 2.0)

  Ruby tools for computational molecular biology

• dep: ruby-fixwhich (>= 1.0.2)

  ruby module that emulates the 'which' program

• dep: ruby-threach (>= 0.2.0)

  Threaded each

• dep: ruby-trollop (>= 2.0)

  command-line argument processing library

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