Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/LiveSeq/IO/README @ 0:1f6dce3d34e0
Uploaded
author | mahtabm |
---|---|
date | Thu, 11 Apr 2013 02:01:53 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/LiveSeq/IO/README Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,27 @@ +# $Id: README,v 1.3 2002/03/15 12:46:43 heikki Exp $ + +README for Bio::LiveSeq::IO + +LiveSeq objects representing known gene structures and their sequences +have to be created from nucleotide sequence files. The current IO +files do it by reading in EMBL entries and parsing out sequences as +well as CDS, exon and primary_transcript features from the feature +table. + +Bio::LiveSeq::IO::Loader + + is a superclass holding methods common to other methods. + +Bio::LiveSeq::IO::BioPerl + + is the preferred method which uses Bio::DB::EMBL to retrive + sequences over the Web by accession number. + +Bio::LiveSeq::IO::SRS + + retrieves sequences from a local installation of SRS. It needs + srsperl.pm which is part of SRS. SRS is short for Sequence + Retrieval System, a comprehensive program suite for indexing + and serving biological databases. SRS is a product of Lion + BioSciences (http://www.lionbio.co.uk/). The license for + academic users is free.