- Derived sequence generation
- $dbu->generateDerivedForms([skipIsoforms=>1][, skipChains=>1][, skipPeptides=>1][, shortName=>1])
- $dbu->seqSubstr(from=>int, to=>int [, subseq=>AAstring]);
- $dbu->seqSubstr(pos=>int, len=>int [, subseq=>AAstring]);
- $dbu->seqExtract(from=>int, to=>int);
- $dbu->seqExtract(pos=>int, len=>int);
- SEE ALSO
InSilicoSpectro::Databanks::DBEntryUniprot - Uniprot formated entry
Inherit from DBEntry, but can parse a uniprot format
determine if InSilicoSpectro lib is used in the current environment. The main difference will be the tracnslation from uniprot MOD_RES nomenclature to InSilciSpectro one
get a ref to an array of arrays for chain delimiter [from, to]
set chain (through a reference a to an array)
Reset the chain arrays
Idem than for the *chain subs
returns an array of InSilicoSpectro::Databanks::DBEntry containing all the isoforms generated by a swissprot entry
Retuns an array of InSilicoSpectro::Databanks::DBEntry containing entries from FT CHAIN lines
Retuns an array of InSilicoSpectro::Databanks::DBEntry containing entries from FT PEPTIDE lines
Retuns an array of InSilicoSpectro::Databanks::DBEntry containing entries from the concatenation of the above methods
skip* argument will skip the creaion of the mentionned form
Replace a piece of the sequence by a a subseq (or remove it if sebseq is unfdefined). All annotation will be updated (or remove if they inerfer with the substitued sequence.
from=>int notation starts sequence at position 1;
pos=>int notation starts sequence at position 0;
Keep only the sub sequence described par the given delimiters (see seqSubstr(...) for description)
read info from fasta contents (fitrs line with '>' and info + remaining is sequence.
Copyright (C) 2004-2005 Geneva Bioinformatics www.genebio.com
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Alexandre Masselot, www.genebio.com