Linxe's eye

Ayer deje abierta mi sesión en un cluster remoto, después de un rato de inactividad esta termino la sesión, pero antes de cerrarse me toco ver estos mensajes, supongo que por el sistema de mensajes del MPI y no tengo idea de quien los mando: Broadcast message from clase_distribuidos_itesm4 (pts/8) (Mon Feb 22 19:58:07Dominaremos el mundo con pthreads Broadcast message from clase_distribuidos_itesm13 (pts/14) (Mon Feb 22 19:58:callate Broadcast message from clase_distribuidos_itesm4 (pts/8) (Mon Feb 22 19:58:37Callame Broadcast message from clase_distribuidos_itesm18 (pts/18) Mon Feb 22 19:58:bye }^_ Broadcast message from clase_distribuidos_itesm17 (pts/19) Mon Feb 22 20:25:largate a Canad? Me gusto el largate a Canadá, sobre todo con los olímpicos que hay ahora. Eso me recuerda que varios programadores en su etapa de aprendizaje son bastante ocurrentes (y mal hablados) en sus primeros pininos de código.

I needed to test some sequence for known TFBS, I was looking for: (1) a public database of TFBS and (2) a program to search the motifs in a sequence(s). First I found Jaspar as an alternative to the commercial TransFac DB , I downloaded the matrices for vertebrate. The second problem was to find a program to search the motifs in any sequence, I did not find any updated program (many are published, but few websites are active nowadays). So, I decided to write my own program, I share the code if anyone can use it: #!/usr/bin/perl -w use strict; use Getopt::Long; =head1 NAME jasparScan.pl =head1 USAGE jasparScan.pl -f FASTA -m MATRIX [-s MODELS] [-c CUT_OFF] OPTIONS: -h --help Help screen -f --fasta Fasta file to scan -m --matrix Jaspar motif matrix -s --models List of models, separated by ':' [Def: all] -c --cutoff Similarity cut-off [Def: 0.90] =head1 DESCRIPTION Script to map a TF binding site matrix (from Jaspar DB) into a fasta sequence. The simila...