Module: compass Description: Comparison Of Motif Predictions Across Sequences/Servers Version: 2.2 Last Edit: 19/05/06

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

Imported modules: rje rje_seq rje_tm rje_uniprot

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

Function

Outputs a table of Scansite predictions etc as arranged by alignment > *.compass.tdt. This file should then be opened using the COMPASS.xls Excel workbook for analysis using its Macros.

This is designed to compare multiple aligned sequences - typically orthologues - and/or multiple servers for making the same kinds of predictions. Although explicitly designed with certain servers (eg. scansite, netphos) in mind, any data that is presented in the right format can be uploaded and compared. The 'Server' column of the results takes its values from the extension of the input files. E.g. *.scansite will have the server 'scansite'.

Input files

- sequence alignment (may be one sequence)
- *.server or *.server.txt server results

Commandline

seqin=FILE : Input alignment file
partial=T/F : Allow partial scansite results (NULL values) [False]
autorun=T/F : Automated querying of web servers (within RCSI only) [False]
results=T/F : Whether to output summary file or simply check/generate results (Aligned seqs only) [True]
recase=T/F : Whether to look for accession numbers in case-independent fashion (scansite results) [True]
txt=T/F : Whether to look by deafult for *.server.txt files (True) or *.server files (False) [True]
scansite=FILE : Motif prediction files for sequences in scansite format [*.scansite, *.automotif & *.elm]
netphos=FILE : Motif prediction files for sequences in netphos format [*.netphos]
uniprot=FILE : Sequence features/details in UniProt download format [*.uniprot]
tmhmm=FILE : Transmembrane topology data in TMHMM single-line format [*.tmhmm]
signalp=FILE : SignalP results in single-line format [*.signalp]
serverlist=X,Y,..,Z : List of servers for results to be read from
['scansite','netphos','automotif','elm','uniprot','tmhmm','signalp','antigenic','disorder']