Commit 6861dc51 authored by Elias Dohmen's avatar Elias Dohmen

version 2.0

parent 39d59009
DOGMA 2.0
=========
- added reference sets for bacteria, archae
- expanded support for different Pfam versions
- usage of order for UProC (proteome only)
- removing clan collapse
DOGMA
====
DOGMA is a program for fast and easy quality assessment of
transcriptome and proteome data based on conserved protein domains.
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/)
OR
- pfam_scan.pl (ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/)
Furthermore you will need a core set to run DOGMA.
We provide several precomputed core sets for different clades here:
http://domainworld.uni-muenster.de/DOGMA.html
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).
Usage
-----
Please take a look at the User Manual for a detailed description.
Citation
--------
If you used DOGMA in your project please cite our publication:
Elias Dohmen, Lukas P.M. Kremer, Erich Bornberg-Bauer, and Carsten Kemena, DOGMA: domain-based transcriptome and proteome quality assessment,
Bioinformatics (2016) 32 (17): 2577-2581, first published online May 5, 2016, doi:10.1093/bioinformatics/btw231
http://bioinformatics.oxfordjournals.org/content/32/17/2577
Problems, Bugs & Suggestions
----------------------------
We try our best not to have any bugs in the code, unfortunately some will
probably avoid us and will not be detected.
If you encounter one, please be so kind and let us know.
Also if you have any questions feel free to contact us by email:
Elias Dohmen (e.dohmen[ at ]uni-muenster.de) or
Carsten Kemena (c.kemena[ at ]uni-muenster.de)
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