Mercurial > repos > willmclaren > ensembl_vep

view variant_effect_predictor/Bio/LiveSeq/IO/README @ 1:d6778b5d8382 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author willmclaren
date Fri, 03 Aug 2012 10:05:43 -0400
parents 21066c0abaf5
children
line wrap: on
line source

# $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.