Author image Alexandre Masselot
and 1 contributors


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



describes an databnk entry (header + sequence)



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



get/set accession code


get/set accession ID


[GS]et databank name


[GS]et taxonomy if (typically NCBI taxid



Get/Set AC, ID, ...


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


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


remove all Variants



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


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


Print the entry under a html format.




Copyright (C) 2004-2005 Geneva Bioinformatics

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,