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rje_tm V1.2

Tranmembrane and Signal Peptide Prediction Module

Module: rje_tm
Description: Tranmembrane and Signal Peptide Prediction Module
Version: 1.2
Last Edit: 16/08/07

Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_seq rje_zen


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

Function

Will read in results from tmhmm and/or signalp files as appropriate and append output to: - tm.tdt = TM domain counts and orientation - domains.tdt = Domain table - singalp.tdt = SingalP data (use to add signal peptide domains to domains table using mySQL

Commandline

tmhmm=FILE : TMHMM output file [None]
signalp=FILE: SignalP output file [None]
mysql=T/F : Output results in tdt files for mySQL import [True]
seqin=FILE : Sequence file for which predictions have been made [None]
maskcleave=T/F : Whether to output sequences with cleaved signal peptides masked. [False]
source=X : Source text for mySQL file ['tmhmm']

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Basic functional version.
    # 1.1 - Output of 'truncated' proteins - cleaved signalp peptides replaced with Xs.
    # 1.2 - Added standalone parsing methods as first step in development (& for rje_ensembl.ensDat())

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