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VDJFasta

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5.0 Stars (5)
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Download vdjfasta-1.1.2.tgz
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Description

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. Suitable for mammalian repertoire sequences obtained either by Sanger or 454 sequencing. Methods published in Glanville, Zhai, Berka et al, PNAS 2009.

VDJFasta Web Site

Features

  • HMM-based CDR identification
  • HMM-based translation and alignment
  • Probabilistic germline classification

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ease 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 4 / 5
features 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 4 / 5
design 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 4 / 5
support 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 3 / 5
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User Reviews

  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    change the combination calculation funtion, i.e. nCk, to sub combination { my( $n, $k ) = @_; return unless defined $n && $n =~ /^\d+$/ && defined $k && $k =~ /^\d+$/; my $product = 1; while( $k > 0 ) { $product *= $n--; $product /= $k--; } return $product; } as in Math/Counting.pm get 30% of speedup!

    Posted 11/16/2015
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    The software is great, but be aware there is a mistake in the README file. It tells you to point to the program 'blastall' when setting $self->{blast} = "/location/of/blastall" but actually you need to point to 'blastn' not 'blastall'. The the program works fine. Good job!

    Posted 01/30/2014
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Vdjfasta is great! Thanks.

    Posted 06/23/2013
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    This core module enables a variety of sophisticated antibody analysis.

    Posted 03/03/2011
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Additional Project Details

Intended Audience

Science/Research

User Interface

Console/Terminal

Programming Language

Perl

Registered

2011-02-28

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