Freecontact

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Freecontact

http://rostlab.org/
fast protein contact predictor

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 command line tool freecontact(1).





Licensing

License

Verified by

Verified on

Notes

Verified by

Debian: Laszlo Kajan <lkajan@debian.org>

Verified on

25 February 2014

Notes

License: gpl-3+




Leaders and contributors

Contact(s)Role
Laszlo Kajan contact


Resources and communication

AudienceResource typeURI
Downloadftp://rostlab.org/free/
Debian (Ref)https://tracker.debian.org/pkg/freecontact


Software prerequisites

This entry (in part or in whole) was last reviewed on 14 February 2018.



Entry




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Date 2015-07-17
Source Debian
Source link http://packages.debian.org/sid/freecontact

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