Package: freecontact (1.0.21-13)

[ Source: freecontact  ]

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).

Other Packages Related to freecontact

• dep: libboost-program-options1.74.0 (>= 1.74.0+ds1)

  program options library for C++

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libfreecontact0v5 (>= 1.0.21)

  fast protein contact predictor library

• dep: libgcc-s1 (>= 3.0) [not armel, armhf]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libstdc++6 (>= 11)

  GNU Standard C++ Library v3

• dep: libxerces-c3.2

  validating XML parser library for C++

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• sug: bash-completion

  programmable completion for the bash shell

• sug: hhsuite

  sensitive protein sequence searching based on HMM-HMM alignment

• sug: hmmer

  profile hidden Markov models for protein sequence analysis

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