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Paket: python-freecontact (1.1-2build4)

fast protein contact predictor - binding for Python

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 Python binding.

Andra paket besläktade med python-freecontact

  • beror
  • rekommenderar
  • föreslår
  • dep: libboost-python1.65.1
    Boost.Python Library
  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    också ett virtuellt paket som tillhandahålls av libc6-udeb
    dep: libc6 (>= 2.4) [i386]
  • dep: libfreecontact0v5
    fast protein contact predictor library
  • dep: libgcc1 (>= 1:3.0)
    GCC support library
  • dep: libstdc++6 (>= 5)
    GNU Standard C++ Library v3
  • dep: python
    interactive high-level object-oriented language (default version)
    dep: python (<< 2.8)
    dep: python (>= 2.7~)

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Arkitektur Paketstorlek Installerad storlek Filer
amd64 77,3 kbyte165 kbyte [filförteckning]
i386 79,0 kbyte160 kbyte [filförteckning]