How can I modify the Smith-Waterman algorithm using substitution matrix to align proteins in Perl?
How can I modify the Smith-Waterman algorithm using a substitution matrix to align proteins in Perl? [citations needed] ...
bioperl
multiFASTA file processing
Hi all, I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe automatically draw descriptive plots. Also an R BIoconductor solution or a BioPerl module would do, but I didn't manage to find anyth...
Is there a Bioperl equivalent of IO::ScalarArray for array of Seq objects?
In Perl, we have IO::ScalarArray for treating the elements of an array like the lines of a file. In BioPerl, we have Bio::SeqIO, which can produce a filehandle that reads and writes Bio::Seq objects instead of strings representing lines of text. I would like to do a combination of the two: I would like to obtain a handle that reads succe...
How can I save BioPerl sequence nested features in genbank or embl format?
EDIT: Please close this question. I asked and got an answer for it on BioStar here. In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that ar...
How to get all feature in a range from a GFF3 file in Perl?
I would like to write a Perl function that gets a GFF3 filename and a range (i.e. 100000 .. 2000000). and returns a reference to an array containing all names/accessions of genes found in this range. I guess using bioperl will make sense, but I have very little experience with it. I can write a script that parses a GFF3 by my self, but ...
How do I install the latest BioPerl version when using perlbrew?
I'm using perlbrew and I would like to install the latest bioperl version. Should I use cpanm or git? If git - do I just install as usual (AKA git clone ... then make and build), or should I do anything special? UPDATE Specifically, I'm not sure I understand the following expert from BioPerl Using Git manual: Tell perl where to fi...
Why won't Eclipse recognize $PERL5LIB?
I followed BioPerl manual: I cloned a fresh copy of bioperl-live under ~/src then added the following line to my ~/.profile (I'm using Ubuntu): export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB" However,BioPerl modules are not recognized in Eclipse, e.g.: Can't locate Bio/Tools/GFF.pm in @INC (@INC contains: /home/dave/workspace/.m...
How do I solve this BioPerl-related mystery?
I'm using Ubuntu 10.04 and Perl 5.10.1. The BioPerl package has some nice scripts, such as bp_genbank2gff3.pl which converts files from genbank format to GFF3 format. The problem: I get unexpected results when using bp_genbank2gff3.pl: the gene features get "Name=" instead of "locus_tag=" in the last GFF3 column. A dear BioPerl mailing...
Perl and bioperl
have worked on a humble projct, I cant use the bioperl on windows 7 how can i do this?* ...
Remove Perl modules from CPAN on Mac
As far as I know it is required to run CPAN with sudo on Mac sudo perl -MCPAN -e shell to install new modules. Theoretically, a module can be removed by deleting it from the Perl folders. My question is: Where are Perl modules put when installed from CPAN with 'sudo' and without 'sudo'? I installed BioPerl both ways and it seemed to ...