Alexandre Masselot > InSilicoSpectro-Databanks > InSilico::Databanks::DBEntry

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NAME ^

InSilico::Databanks::DBEntry - fasta databank entry + header's annotated info

SYNOPSIS ^

DESCRIPTION ^

describes an databnk entry (header + sequence)

FUNCTIONS ^

METHODS ^

my $dbe=InSilico::Databanks::DBEntry->new([\%h]);

Accessors/Setters

$dbe->AC([val])

get/set accession code

$dbe->ID([val])

get/set accession ID

$dbe->dbName([val])

[GS]et databank name

$dbe->taxoID([val])

[GS]et taxonomy if (typically NCBI taxid

$dbe->description([val])

$dbe->sequence([val])

Get/Set AC, ID, ...

$dbe->seqType(["AA"|"DNA"])

Get or set the sequence type

$dbe->annotatedModRes(string|[[pos1, mod1], [pos2, mod2]]);

get or set annotated PTM from a string (e.g. (1|ACET_nterm)(2|ACET_nterm)(185|PHOS)) or an array. All previously set TPM are removed

$dbe->add_annotatedModRes(pos, modkey)

add an annotated PTM

$dbe->clear_annotatedModRes()

remove all annotated modres

$dbe->variants(string|[[pos1, seq1a, seq1b], [pos2, seq2a, seq2b]]);

get or set variant a string (e.g. ("(9|F|Y)(30|D|N)(41|A|G)(43|Q|R)") or an array. All previously set TPM are removed

$dbe->add_variant(pos, seqa, seqb)

add a VARIANT, replacing seqa by seqb (often just one aminoacid) at pos

$dbe->clear_variants()

remove all Variants

I/O

$dbe->readFasta($fastacontent);

read info from fasta contents (fitrs line with '>' and info + remaining is sequence.

$dbe->printFasta();

print the entry under fasta format (use SelectSaver or whatever select method to redirect towards a file descriptor);

$dbe->printHtml();

Print the entry under a html format.

EXAMPLES ^

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

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