HPRD Database processing module
Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
This module is designed for specific PPI Database manipulations:
1. Parsing HPRD Flat Files. [This is the default and is run if no other option is selected.]
>Gene_HUMAN__AccNum Description [Gene:WWWW HPRD:XXXX; gb:YYYY; sp:ZZZZ]
2. Converting a table of interactions into a distance matrix. This table should be a plain text file in which the first column is the interacting protein name and the subsequent columns are for the proteins (hubs) to be clustered. The first row contains their name. The rows for each spoke protein should be empty (or value 0) if there is no interaction and have a non-zero value if there is an interaction: Gene Beta Epsilon Eta Gamma Sigma Theta Zeta AANAT 1
A distance matrix is then produced (
3. Incorporation of data from the GeneCards website (and Human EnsLoci) using rje_genecards. This will create a file
called HPRD.genecards.tdt by default but this can be over-ridden using
### HRPD Options ###
History Module Version History
# 1.0 - Working version based on rje_ppi. # 1.1 - Added protein complexes and PPI Types. # 1.2 - Added tracking of evidence. # 1.2.1 - Fixed "PROTEIN_ARCHITECTURE" bug.
© 2015 RJ Edwards. Contact: email@example.com.