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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.
Features
- HMM-based CDR identification
- HMM-based translation and alignment
- Probabilistic germline classification
Categories
Bio-InformaticsLicense
Academic Free License (AFL)Follow VDJFasta
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User Reviews
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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!
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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!
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Vdjfasta is great! Thanks.
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This core module enables a variety of sophisticated antibody analysis.