BioPerl FAQ (Frequently Asked Questions)

Are you a biotech professional? Need to update your biotech knowledge or need to prepare for a job interview? Check out this collection of BioPerl FAQ (Frequently Asked Questions)...

What is included in this FAQ?
What is this FAQ?
How is it maintained?
How can I tell what version of BioPerl is installed?
What is BioPerl?
Where do I go to get the latest release?
What is the difference between 1.5.1 and 1.4.0? What do you mean developer release?
How can I learn how to use a module?
I'm interested in the bleeding edge version of the code, where can I get it?
Who uses this toolkit?
How should I cite BioPerl?
What are the license terms for BioPerl?
I want to help, where do I start?
I've got an idea for a module how do I contribute it?
How do I submit a patch or enhancement to BioPerl?
Why can't I easily get a list of all the methods a object can call?
Can you explain the Object Model design and rationale?
How do I parse a sequence file?
I can't get sequences with Bio::DB::GenBank any more, why not?
How can I get NT_ or NM_ or NP_ accessions from NCBI (Reference sequences)?
How can I use Bio::SeqIO to parse sequence data to or from a string?
How do I use Bio::Index::Fasta and index on different ids?
Cannot get an accession from GenBank when I know it is there
Accession numbers are not present for FASTA sequence files
How do I get genomic sequences when all I have is an gene identifier or name?
I would like to make my own custom fasta header - how do I do this?
I want to parse BLAST, how do I do this?
What was wrong with Bio::Tools::Blast?
I want to parse FASTA or NCBI -m7 (XML) format, how do I do this?
How can I generate a pairwise alignment of two sequences?
How do I get the frame for a translated search?
Can I get domain number from hmmpfam or hmmsearch output?
Does Bio::SearchIO parse the HTML output that BLAST creates using the -T option?
How do I retrieve all the features from a sequence?
How do I parse the CDS join or complement statements in GenBank or EMBL files to get the sub-locations?
How do I retrieve a nucleotide coding sequence when I have a protein gi number?
How do I get the complete spliced nucleotide sequence from the CDS section?
How do I get the reverse-complement of a sequence using the subseq method?
I get the warning (old style Annotation) on new style Annotation::Collection. What is wrong?
How do I find all the ORFs in a nucleotide sequence? Antigenic sites in a protein? Calculate nucleotide melting temperature? Find repeats?
How do I do motif searches with BioPerl? Can I do "find all sequences that are 75% identical" to a given motif?
Can I query MEDLINE or other bibliographic repositories using BioPerl?
How do I merge a set of sequences along with their features and annotations?
How do I run BLAST from within BioPerl?
How do I tell BLAST to search multiple database using Bio::Tools::Run::StandAloneBlast?
Hey, I want to run Clustalw within BioPerl, I used Bio::Tools::Run::Alignment::Clustalw before - where did it go?
What does the future hold for running applications within BioPerl?
I'm trying to run Bio::Tools::Run::StandAloneBlast and I'm seeing error messages like Can't locate Bio/Tools/Run/WrapperBase.pm - how do I fix this?
What is bioperl-ext?
bioperl-ext won't compile the staden IO lib part - what do I do?
What is bioperl-db?
What is bioperl-microarray?
What is bioperl-gui?
What is bioperl-pedigree?