Commit 95c6e86a authored by Elias Dohmen's avatar Elias Dohmen 🎓

DOGMA Version 3

parent 2bd3a924
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
......@@ -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)
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