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[ Source: freecontact  ]

Package: freecontact (1.0.21-13)

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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).

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Architecture Package Size Installed Size Files
amd64 360.1 kB1,734.0 kB [list of files]
arm64 324.7 kB1,698.0 kB [list of files]
armel 309.5 kB1,537.0 kB [list of files]
armhf 313.2 kB1,257.0 kB [list of files]
i386 372.4 kB1,781.0 kB [list of files]
mips64el 349.5 kB2,443.0 kB [list of files]
mipsel 348.7 kB2,281.0 kB [list of files]
ppc64el 357.8 kB2,082.0 kB [list of files]
s390x 325.3 kB1,758.0 kB [list of files]