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Biotech
> FAQ > BioPerl FAQ (Frequently Asked Questions)
To see other biotech frequently asked questions,
please visit http://biotech.fyicenter.com/faq/
What is included in this FAQ?
- 1 About this FAQ
- 1.1 What is this FAQ?
- 1.2 How is it maintained?
- 1.3 How can I tell what version of BioPerl is installed?
- 2 BioPerl in General
- 2.1 What is BioPerl?
- 2.2 Where do I go to get the latest release?
- 2.3 What is the difference between 1.5.1 and 1.4.0? What do you mean developer release?
- 2.4 How can I learn how to use a module?
- 2.5 I'm interested in the bleeding edge version of the code, where can I get it?
- 2.6 Who uses this toolkit?
- 2.7 How should I cite BioPerl?
- 2.8 What are the license terms for BioPerl?
- 2.9 I want to help, where do I start?
- 2.10 I've got an idea for a module how do I contribute it?
- 2.11 How do I submit a patch or enhancement to BioPerl?
- 2.12 Why can't I easily get a list of all the methods a object can call?
- 2.13 Can you explain the Object Model design and rationale?
- 3 Sequences
- 3.1 How do I parse a sequence file?
- 3.2 I can't get sequences with Bio::DB::GenBank any more, why not?
- 3.3 How can I get NT_ or NM_ or NP_ accessions from NCBI (Reference sequences)?
- 3.4 How can I use Bio::SeqIO to parse sequence data to or from a string?
- 3.5 How do I use Bio::Index::Fasta and index on different ids?
- 3.6 Cannot get an accession from GenBank when I know it is there
- 3.7 Accession numbers are not present for FASTA sequence files
- 3.8 How do I get genomic sequences when all I have is an gene identifier or name?
- 3.9 I would like to make my own custom fasta header - how do I do this?
- 4 Report Parsing
- 4.1 I want to parse BLAST, how do I do this?
- 4.2 What was wrong with Bio::Tools::Blast?
- 4.3 I want to parse FASTA or NCBI -m7 (XML) format, how do I do this?
- 4.4 How can I generate a pairwise alignment of two sequences?
- 4.5 How do I get the frame for a translated search?
- 4.6 Can I get domain number from hmmpfam or hmmsearch output?
- 4.7 Does Bio::SearchIO parse the HTML output that BLAST creates using the -T option?
- 5 Annotations and Features
- 5.1 How do I retrieve all the features from a sequence?
- 5.2 How do I parse the CDS join or complement statements in GenBank or EMBL files to get the sub-locations?
- 5.3 How do I retrieve a nucleotide coding sequence when I have a protein gi number?
- 5.4 How do I get the complete spliced nucleotide sequence from the CDS section?
- 5.5 How do I get the reverse-complement of a sequence using the subseq method?
- 5.6 I get the warning (old style Annotation) on new style Annotation::Collection. What is wrong?
- 6 Utilities
- 6.1 How do I find all the ORFs in a nucleotide sequence? Antigenic sites in a protein? Calculate nucleotide
melting temperature? Find repeats?
- 6.2 How do I do motif searches with BioPerl? Can I do "find all sequences that are 75% identical" to a given
motif?
- 6.3 Can I query MEDLINE or other bibliographic repositories using BioPerl?
- 6.4 How do I merge a set of sequences along with their features and annotations?
- 7 Running external programs
- 7.1 How do I run BLAST from within BioPerl?
- 7.2 How do I tell BLAST to search multiple database using Bio::Tools::Run::StandAloneBlast?
- 7.3 Hey, I want to run Clustalw within BioPerl, I used Bio::Tools::Run::Alignment::Clustalw before - where did it
go?
- 7.4 What does the future hold for running applications within BioPerl?
- 7.5 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?
- 8 Other BioPerl packages
- 8.1 What is bioperl-ext?
- 8.2 bioperl-ext won't compile the staden IO lib part - what do I do?
- 8.3 What is bioperl-db?
- 8.4 What is bioperl-microarray?
- 8.5 What is bioperl-gui?
- 8.6 What is bioperl-pedigree?
(Continued on next question...)
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