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Pakket: freecontact (1.0.21-6build2)

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).

Andere aan freecontact gerelateerde pakketten

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  • 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

freecontact downloaden

Pakket downloaden voor alle beschikbare platforms
Platform Pakketgrootte Geïnstalleerde grootte Bestanden
amd64 333,6 kB1630 kB [overzicht]
i386 344,7 kB1693 kB [overzicht]