NAME
InSilicoSpectro::Databanks::DBEntryUniprot
SYNOPSIS
DESCRIPTION
Inherit from DBEntry, but can parse a uniprot format
FUNCTIONS
useInSilicoSpectro()
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
METHODS
my $dbu=InSilicoSpectro::Databanks::DBEntryUniprot;
Accessors/Setters
$dbu->chains()
get a ref to an array of arrays for chain delimiter [from, to]
$dbu->add_chain([$from, $to])
set chain (through a reference a to an array)
$dbu->clear_chains()
Reset the chain arrays
$dbu->signals(); $dbu->add_signal([$from, $to]); $dbu->clear_signals()
Idem than for the *chain subs
Derived sequence generation
$dbu->generateIsoforms(shortName)
returns an array of InSilicoSpectro::Databanks::DBEntry containing all the isoforms generated by a swissprot entry
$dbu->generateChains(shortName)
Retuns an array of InSilicoSpectro::Databanks::DBEntry containing entries from FT CHAIN lines
$dbu->generatePeptides(shortName)
Retuns an array of InSilicoSpectro::Databanks::DBEntry containing entries from FT PEPTIDE lines
$dbu->generateDerivedForms([skipIsoforms=>1][, skipChains=>1][, skipPeptides=>1][, shortName=>1])
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
$dbu->seqSubstr(from=>int, to=>int [, subseq=>AAstring]);
$dbu->seqSubstr(pos=>int, len=>int [, subseq=>AAstring]);
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;
$dbu->seqExtract(from=>int, to=>int);
$dbu->seqExtract(pos=>int, len=>int);
Keep only the sub sequence described par the given delimiters (see seqSubstr(...) for description)
I/O
$dbe->readDat($fastacontent);
read info from fasta contents (fitrs line with '>' and info + remaining is sequence.
EXAMPLES
EXPORT
$VERBOSE
verbose level
SEE ALSO
COPYRIGHT
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
AUTHORS
Alexandre Masselot, www.genebio.com