|Description:|| Fake UniProt DAT File Generator|
|Last Edit:|| 17/04/12|
Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation.
This program runs a number of in silico predication programs and converts protein sequences into a fake UniProt DAT
flat file. Additional features may be given as one or more tables, using the
features=LIST option. Please see the
UniFake Manual for more details.
seqin=FILE : Input sequence file. See rje_seq documentation for filtering options. [
spcode=X : Species code to use if it cannot be established from sequence name [
features=LIST : List of files of addtional features in delimited form 
aliases=FILE : File of aliases to be added to Accession number list (for indexing) [
pfam=FILE : PFam HMM download [
unipath=PATH : Path to real UniProt Datafile (will look here for DB Index file made with rje_dbase)
unireal=LIST : Real UniProt data to add to UniFake output [
fudgeft=T/F : Fudge the real features left/right until a sequence match is found [
unifake=LIST : List of predictions to add to entries [
datout=FILE : Name of output DAT file [
Default input FILE.dat]
disdom=X : Disorder threshold below which to annotate PFam domain as "DOMAIN" [
makeindex=T/F : Whether to make a uniprot index file following run [
ensdat=T/F : Look for acc/pep/gene in sequence name [
tmhmm=FILE : Path to TMHMM program [
cleanup=T/F : Remove TMHMM files after run [
signalp=FILE : Path to SignalP program [
History Module Version History
# 0.0 - Initial Compilation.
# 1.0 - Version with full functionality.
# 1.1 - Made changes to temp file names for parallel running
# 1.2 - Added option for reading in Features and limited other info from real UniProt entry
# 1.3 - Removed searching in UniProt if not UniReal features given.