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Balík: ruby-crb-blast (0.6.9-1)

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.

Ostatné balíky súvisiace s balíkom ruby-crb-blast

  • závisí
  • odporúča
  • navrhuje
  • dep: ncbi-blast+
    next generation suite of BLAST sequence search tools
  • dep: ruby
    Interpreter of object-oriented scripting language Ruby (default version)
    alebo ruby-interpreter
    Balík nie je dostupný
  • dep: ruby-bio
    Ruby tools for computational molecular biology
  • dep: ruby-fixwhich
    ruby module that emulates the 'which' program
  • dep: ruby-threach
    Threaded each
  • dep: ruby-trollop (>= 2.0)
    command-line argument processing library

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