软件包：freecontact（1.0.21-13.1 以及其他的） [debports]
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).
其他与 freecontact 有关的软件包
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- dep: libboost-program-options1.83.0 (>= 1.83.0)
- program options library for C++
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- dep: libc6.1 (>= 2.37)
- GNU C 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6.1-udeb
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- dep: libfreecontact0t64 (>= 1.0.21)
- fast protein contact predictor library
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- dep: libstdc++6 (>= 13.1)
- GNU 标准 C++ 库，第3版
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- dep: libunwind8
- library to determine the call-chain of a program - runtime
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- dep: libxerces-c3.2t64
- validating XML parser library for C++
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- dep: perl
- 拉里 沃尔的实用报表提取语言(Perl)
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- sug: bash-completion
- bash shell 的可编程补全
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- sug: hhsuite
- sensitive protein sequence searching based on HMM-HMM alignment
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- sug: hmmer
- profile hidden Markov models for protein sequence analysis