Module: rje_yeast Description: Yeast PPI & Sequence Module Version: 0.0 Last Edit: 22/12/10

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_seq rje_sequence rje_uniprot rje_zen rje_blast_V1

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This Yeast SLiMFinder Analysis Module is designed to read, assess, store and combine the different yeast information for SLiMFinder analysis, using the YGOB for generating alignments for conservation masking etc.

The main (default) inputs are: - Y2H_union.txt = High quality binary interactions from Vidal lab - Pillars.tab = YGOB orthology pillars for yeast species - Proteins.fas = Fasta file of protein sequences to match pillars.tab

Commandline

INPUT DATA

seqin=FILE : Input sequence file containing yeast sequences [Proteins.fas]
pillars=FILE : YGOB pillars file [Pillars.tab]
ppifile=FILE : Input PPI data (two columns of binary interactors) [Y2H_union.txt]
xref=FILE : Yeast identifier XRef file (e.g. BioMart download) [yeast_xref.20101222.tdt]
sgd2sp=T/F : Convert SGD identifiers into SwissProt identifiers [False]
gopher=T/F : Whether to feed Pillars into GOPHER Orthology (at BLAST ID stage) [False]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.