Paketti: freecontact (1.0.21-9)

[ 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).

Muut pakettiin freecontact liittyvät paketit

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

  program options library for C++

• dep: libc6 (>= 2.17)

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6-udeb

• dep: libfreecontact0v5 (>= 1.0.21)

  fast protein contact predictor library

• dep: libgcc-s1 (>= 3.0)

  GCC:n apukirjasto

• dep: libstdc++6 (>= 9)

  GNU standardi C++ -kirjasto, versio 3

• dep: libxerces-c3.2

  validating XML parser library for C++

• dep: perl

  Larry Wallin kieli tekstitiedostojen analysointia ja raportointia varten

• sug: bash-completion

  ohjelmoitava täydentäjä bash-komentotulkille

• 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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