Skip to content
Sections
>> Trisquel >> Packages >> etiona >> python >> python-freecontact
[  etiona  ]
[ Source: python-freecontact  ]

Package: 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.

Other Packages Related to python-freecontact

  • depends
  • recommends
  • suggests

Download python-freecontact

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 77.3 kB165 kB [list of files]
i386 79.0 kB160 kB [list of files]