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rje_slimfungo V0.0

SLiM Functional GO classification module

Module: rje_slimfungo
Description: SLiM Functional GO classification module
Version: 0.0
Last Edit: 28/03/08

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


Imported modules: rje rje_seq rje_go rje_zen


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

Function

This module sticks together GO categories with output from SLiMSearch to try and assess functional significance within categories.

Commandline

occdata=FILE : File of motif occurrences. Must have [None]
gomap=FILE : Mapping of sequences to GO categories [None]
minocc=X : Min occurrences for a motif in a GO category [6]

Optional

seqin=FILE : File of input sequences [None]

RJE_GO Commandline

obofile=FILE : Input GO OBO V1.2 download [None]
webobo=T/F : Whether to download from GO website if file not given [True]
goslim=LIST : List of GO IDs to form basis of GO Slim []

History Module Version History

    # 0.0 - Initial Compilation.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.