Bug#723747: ITP: libfreecontact-perl -- fast protein contact predictor - binding for Perl
Package: wnpp
Severity: wishlist
Owner: Laszlo Kajan <lkajan@debian.org>
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* Package name : libfreecontact-perl
Version : 0.08
Upstream Author : Laszlo Kajan <lkajan@rostlab.org>
* URL : http://rostlab.org/
* License : GPL-1+ or Artistic
Programming Lang: C, Perl
Description : fast protein contact predictor - binding for Perl
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 Perl binding.
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