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PeptCluster V1.5.3

Peptide Clustering Module

Module: PeptCluster
Description: Peptide Clustering Module
Version: 1.5.3
Last Edit: 18/01/17
Webserver: http://bioware.soton.ac.uk/peptcluster.html

Copyright © 2012 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_aaprop rje_obj rje_pam rje_slim rje_tree rje_zen rje_dismatrix_V2


See SLiMSuite Blog for further documentation.

Function

This program is for simple sequence-based clustering of short (aligned) peptide sequences. First, a pairwise distance matrix is generated from the peptides. This distance matrix is then used to generate a tree using a distance method such as Neighbour-Joining or UPGMA.

Default distances are amino acid property differences loaded from an amino acid property matrix file.

Version 1.5.0 incorporates a new peptide alignment mode to deal with unaligned peptides. This is controlled by the peptalign=T/F/X option, which is set to True by default. If given a regular expression, this will be used to guide the alignment. Otherwise, the longest peptides will be used as a guide and the minimum number of gaps added to shorter peptides. Pairwise peptide distance measures are used to assess different variants, starting with amino acid properties, then simple sequence identity (if ties) and finally PAM distances. One of the latter can be set as the priority using peptdis=X. Peptide alignment assumes that peptides have termini (^ & $) or flanking wildcards added. If not, set termini=F.

Commandline

INPUT OPTIONS

peptides=LIST : These can be entered as a list or file. Lines following '#' or '>' ignored [peptides.txt]
aaprop=FILE : File of amino acid properties [aaprop.txt]
aadis=FILE : Alternative amino acid distance matrix [None]
peptalign=T/F/X : Align peptides. Will use as guide regular expression, else T/True for regex-free alignment. []
termini=T/F : Whether peptides for alignment have termini (^ & $) or X flanking regex match [True]
maxgapvar=X : Maximum number of consecutive gaps to allow for peptide alignment without Regex guide [3]
maxgapx=X : Maximum total number of gaps to allow for peptide alignment without Regex guide [5]

CLUSTER OPTIONS

peptdis=X : Method for generating pairwise peptide distances (id/prop/pam) [prop]
peptcluster=X : Clustering mode (upgma/wpgma/neighbor) [upgma]

OUTPUT OPTIONS

savedis=FILE : Output distance matrix to file [peptides.*]
outmatrix=X : Type for output matrix - tdt / csv / mysql / phylip / png [tdt]
savetree=FILE : Save generated tree as FILE [peptides.peptdis.peptcluster.*]
treeformats=LIST: List of output formats for generated trees (nsf/nwk/text/r/png/bud/qspec/cairo/te/svg/html) [nwk,text]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Initial working version.
    # 1.1 - Modified output a little.
    # 1.2 - CGI Output tuple.
    # 1.3 - PAM clustering and WPGMA.
    # 1.4 - Bug fixes for end of sequence characters and different length peptides.
    # 1.5.0 - Added peptalign=T/F/X function for aligning peptides using regex or minimal gap addition. Added REST.
    # 1.5.1 - Updated REST output. Removed peptide redundancy.
    # 1.5.2 - Improved clarity of warning message.
    # 1.5.3 - Added catching of splitPattern() error during alignment.

PeptCluster REST Output formats

Run with &rest=help for general options. Run with &rest=full to get full server output as text or &rest=format
for more user-friendly formatted output. Individual outputs can be identified/parsed using &rest=OUTFMT for:

peptides = original input peptides
aligned = aligned peptides
matrix = peptide distance matrix
X = peptide tree(s), where X is nsf/nwk/text/png/svg (treeformats=LIST: only nwk & text made by default.)

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