DOGMA Version 3

CHANGELOG

-DOGMA 2.0
+DOGMA 3.0
 =========
 
-- added reference sets for bacteria, archae
-- expanded support for different Pfam versions
-- usage of order for UProC (proteome only)
-- removing clan collapse
+- RADIANT support implemented
+- RADIANT replaces UProC - no UProC annotations supported anymore (also no database updates for UProC)
+- -a parameter for automatic detection of input file format introduced (replaces -p and -u options)
+- -d parameter introduced for RADIANT database path specification if -i parameter is used

README.md

@@ -10,7 +10,7 @@ Requirements
 We try to keep the dependencies as little as possible. 
 Current dependencies are (but you will just need one of them):
 
-- UProC (http://uproc.gobics.de/)
+- RADIANT (http://domainworld.uni-muenster.de/programs/radiant/)
 OR
 - pfam_scan.pl (ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/)
 
@@ -20,9 +20,8 @@ We provide several precomputed core sets for different clades here:
 
 http://domainworld.uni-muenster.de/programs/dogma/
 
-Unfortunately the developers of UProC do not provide databases for the newer pfam versions. 
-We therefore constructed them ourselves and tested them in combination with DOGMA (no warranty for any other use).
-They can be downloaded from our website (see link above).
+
+UProC is not longer supported with DOGMA version 3.0, however the old coresets and databases can still be found on our website http://domainworld.uni-muenster.de/data/uprocdb/
 
 
 Usage
@@ -56,4 +55,3 @@ Elias Dohmen (e.dohmen[ at ]uni-muenster.de) or
 
 Carsten Kemena (c.kemena[ at ]uni-muenster.de)
 
-