Mercurial > repos > mahtabm > ensembl
comparison variant_effect_predictor/Bio/LiveSeq/IO/README @ 0:1f6dce3d34e0
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| author | mahtabm |
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| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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| -1:000000000000 | 0:1f6dce3d34e0 |
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| 1 # $Id: README,v 1.3 2002/03/15 12:46:43 heikki Exp $ | |
| 2 | |
| 3 README for Bio::LiveSeq::IO | |
| 4 | |
| 5 LiveSeq objects representing known gene structures and their sequences | |
| 6 have to be created from nucleotide sequence files. The current IO | |
| 7 files do it by reading in EMBL entries and parsing out sequences as | |
| 8 well as CDS, exon and primary_transcript features from the feature | |
| 9 table. | |
| 10 | |
| 11 Bio::LiveSeq::IO::Loader | |
| 12 | |
| 13 is a superclass holding methods common to other methods. | |
| 14 | |
| 15 Bio::LiveSeq::IO::BioPerl | |
| 16 | |
| 17 is the preferred method which uses Bio::DB::EMBL to retrive | |
| 18 sequences over the Web by accession number. | |
| 19 | |
| 20 Bio::LiveSeq::IO::SRS | |
| 21 | |
| 22 retrieves sequences from a local installation of SRS. It needs | |
| 23 srsperl.pm which is part of SRS. SRS is short for Sequence | |
| 24 Retrieval System, a comprehensive program suite for indexing | |
| 25 and serving biological databases. SRS is a product of Lion | |
| 26 BioSciences (http://www.lionbio.co.uk/). The license for | |
| 27 academic users is free. |