パッケージ: freecontact (1.0.21-15)
freecontact に関するリンク
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外部の資源:
- ホームページ [rostlab.org]
類似のパッケージ:
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).
その他の freecontact 関連パッケージ
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- dep: libboost-program-options1.83.0 (>= 1.83.0)
- C++ 用プログラムオプションライブラリ
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- dep: libc6 (>= 2.38)
- GNU C ライブラリ: 共有ライブラリ
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: libfreecontact0t64 (>= 1.0.21)
- fast protein contact predictor library
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- dep: libgcc-s1 (>= 3.0) [riscv64 以外]
- GCC 共有ライブラリ
- dep: libgcc-s1 (>= 3.4) [riscv64]
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- dep: libstdc++6 (>= 14)
- GNU 標準 C++ ライブラリ v3
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- dep: libxerces-c3.2t64
- validating XML parser library for C++
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- dep: perl
- Larry Wall 作の実用的な抽出とレポート用の言語
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- sug: bash-completion
- bash シェル用のプログラム可能な補完機能
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- sug: hhsuite
- sensitive protein sequence searching based on HMM-HMM alignment
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- sug: hmmer
- タンパク質配列解析用のプロファイル隠れマルコフモデル