Python-freecontact
Python-freecontact
http://rostlab.org/
fast protein contact predictor - binding for Python
FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).
FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.
A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after- weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.
jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.
This package contains the Python binding.
Download
http://ftp.debian.org/debian/pool/main/p/python-freecontact/python-freecontact_1.1.orig.tar.gz
Categories
Licensing
License
Verified by
Verified on
Notes
License
Verified by
Debian: Laszlo Kajan <lkajan@debian.org>
Verified on
17 July 2013
Notes
License: gpl-3+
Leaders and contributors
| Contact(s) | Role |
|---|---|
| Laszlo Kajan | contact |
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Debian (Ref) | https://tracker.debian.org/pkg/python-freecontact | |
| Download | ftp://rostlab.org/free/ |
Software prerequisites
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