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rje_disorder V1.2.1

Disorder Prediction Module

Module: rje_disorder
Description: Disorder Prediction Module
Version: 1.2.1
Last Edit: 19/04/18

Copyright © 2006 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje


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

Function

This module currently has limited function and no standalone capability, though this may be added with time. It is designed for use with other modules. The disorder Class can be given a sequence and will run the appropriate disorder prediction software and store disorder prediction results for use in other programs. The sequence will have any gaps removed.

Currently four disorder prediction methods are implemented:

  • * IUPred : Dosztanyi Z, Csizmok V, Tompa P & Simon I (2005). J. Mol. Biol. 347, 827-839. This has to be installed
  • locally. It is available on request from the IUPred website and any use of results should cite the method. (See http://iupred.enzim.hu/index.html for more details.) IUPred returns a value for each residue, which by default, is determined to be disordered if > 0.5.
    • * FoldIndex : This is run directly from the website (http://bioportal.weizmann.ac.il/fldbin/findex) and more simply
    • returns a list of disordered regions. You must have a live web connection to use this method!
      • * ANCHOR : Meszaros B, Simon I & Dosztanyi Z (2009). PLoS Comput Biol 5(5): e1000376. This has to be installed
      • locally. It is available on request from the ANCHOR website and any use of results should cite the method. (See http://anchor.enzim.hu/ for more details.) ANCHOR returns a probability value for each residue, which by default, is determined to be disordered if > 0.5.
        • * Parse: Parsed disorder from protein sequence name, e.g. DisProt download.
        • #X-Y = disordered region; &X-Y = ordered region [0.0]
          For IUPred, the individual residue results are stored in Disorder.list['ResidueDisorder']. For both methods, the disordered regions are stored in Disorder.list['RegionDisorder'] as (start,stop) tuples.

          V1.2.0 introduced the optional use of IUScoreDir/ to save and/or (re)load lists of disorder scores. These are files named <ACC>.<DISORDER>.txt where <ACC> is the accession number of the protein. If md5acc=T then an md5 hash of the sequence is used instead: hashlib.md5(<SEQUENCE>).hexdigest().

Commandline

### General Options ###
disorder=X : Disorder method to use (iupred/foldindex/anchor/parse) [iupred]
strict=T/F : Whether to exit with error if disorder method not found [False]
iucut=X : Cut-off for score-based method (e.g. IUPred/ANCHOR) results [0.2]
iumethod=X : IUPred method to use (long/short) [short]
sequence=X : Sequence to predict disorder for (autorun) []
name=X : Name of sequence to predict disorder for []
minregion=INT : Minimum length of an ordered/disordered region [0]
minorder=INT : Minimum length of an ordered region; over-rides minregion if >-1 [-1]
smoothing=X : Smoothing mode for minregion=X and minorder=X smoothing (foldfirst/sequence) [foldfirst]
iuscoredir=PATH : Path in which to save protein acc.DISORDER.txt score files for re-use []
discalculate=T/F: Whether to try to calculate disorder if existing score not loaded [True]
md5acc=T/F : Whether to use md5sum hexdigest hashing of sequence in place of accession numbers [False]
### System Settings ###
iupath=PATH : The full path to the IUPred executable [c:/bioware/iupred/iupred.exe]
anchor=PATH : Full path to ANCHOR executable []
filoop=INT : Number of times to try connecting to FoldIndex server [10]
fisleep=INT : Number of seconds to sleep between attempts [2]
iuchdir=T/F : Whether to change to IUPred directory and run (True) or rely on IUPred_PATH env variable [False]

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added parsing of disorder from name as an option instead of disorder prediction
    # 0.2 - Added Folded tuple as well as disordered
    # 0.3 - Added PrintLog opt attribute
    # 0.4 - Added option for correct use of IUPred_PATH environment variable
    # 0.5 - Added Minimum length of an ordered/disordered region
    # 0.6 - Added ANCHOR prediction.
    # 0.7 - Added globProportion calculation.
    # 0.8 - Added makeRegions() method.
    # 1.0.0 - Added random disorder function and elevated to v1.x as fully functional for SLiMSuite
    # 1.1.0 - Added strict option for disorder method selection. Added minorder=X.
    # 1.2.0 - Added saving and loading scores to IUScoreDir/.

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