Author image Alexandre Masselot
and 1 contributors

NAME - shuffle each sequence, without any original tryptic peptide


Reads input fasta file and produce a shuffle databank & avoid known cleaved peptides: shuffle sequence but avoid producing known tryptic peptides


#shuffle each sequence --in=/tmp/uniprot_sprot.fasta

#to limit memory usage, one can use CRC code (--crcsize will ./ --ac-prefix=DECOY_ --in=/home/alex/tmp/a.fasta --out=/tmp/a.fasta --crcsize=33 -v --norandom



An input fasta file (will be uncompressed if ending with gz)


A .fasta file [default is stdout]



Set a key to be prepended before the AC in the randomized bank. By default, it will be dependent on the choosen method.

--peptminlength [default 6]

Set the size of the peptide to be reshuffled if they already exist


Building a hash of known cleaved peptide can be quite demanding for memory (uniprot_trembl => ~4GB). Therefore solution is to make an array containing statements if or not a peptide with corresponding crc code was found.

The argument passed here is the number of bits use for the CRC coding: 33 means 2^33 bit of memory => 2^30 bytes => 1GB


Random generator seed is set to 0, so 2 run on same data will produce the same result



do not display terminal progress bar (if possible)




Setting an environment variable DO_NOT_DELETE_TEMP=1 will keep the temporay file after the script exit



Copyright (C) 2004-2006 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,