Index

NAME
SYNOPSIS
DESCRIPTION
FUNCTIONS
- - useInSilicoSpectro()
METHODS
EXAMPLES
EXPORT
- - $VERBOSE
SEE ALSO
COPYRIGHT
AUTHORS

NAME

InSilicoSpectro::Databanks::DBEntryUniprot - Uniprot formated entry

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

COPYRIGHT

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