Module: ProtHunter Description: Protein Hunter Version: 0.0.0 Last Edit: 29/01/15

Copyright © 2015 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_html rje_obj rje_seqlist

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

Function

ProtHunter is essentially a wrapper for plugging together four processing steps into a single pipeline:

1. Reformatting and/or translating a set of protein/DNA target sequences ready for searching. 2. GABLAM or HMM search of candidate proteins/domains in target sequences. 3. MultiHAQ annotation of candidate targets using additional protein databases. 4. Generation of summary HTML files for easy data exploration.

During development, not all of these functions will be available.

Commandline

INPUT OPTIONS

seqin=SEQFILE # File containing target protein/DNA sequences
candidates=SEQFILE # File containing candidate protein sequences to go hunting for []

OUTPUT OPTIONS

basefile=X # This will control output file names and also be used to pick up later analyses for HTML etc. []

TARGET PROCESSING OPTIONS

HTML OPTIONS

stylesheets=LIST : List of CSS files to use ['http://www.slimsuite.unsw.edu.au/stylesheets/slimhtml.css']

History Module Version History

    # 0.0 - Initial Compilation.