Paket: freecontact (1.0.21-14 och andra)

[ Källkod: freecontact  ]

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).

Andra paket besläktade med freecontact

• dep: libboost-program-options1.83.0 (>= 1.83.0)

  program options library for C++

• dep: libc6 (>= 2.38) [ej alpha, ia64, sh4]

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

  dep: libc6 (>= 2.39) [sh4]

• dep: libc6.1 (>= 2.37) [ia64]

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6.1-udeb

  dep: libc6.1 (>= 2.38) [alpha]

• dep: libfreecontact0t64 (>= 1.0.21)

  fast protein contact predictor library

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, i386, mips64el, ppc64, ppc64el, s390x, x32]

  GCC stödbibliotek

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sh4, sparc64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC stödbibliotek

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC stödbibliotek

• dep: libgomp1 (>= 4.2.1) [sparc64]

  GCC OpenMP (GOMP) support library

• dep: libstdc++6 (>= 13.1) [ia64, m68k]

  GNU standardbibliotek v3 för C++

  dep: libstdc++6 (>= 14) [ej ia64, m68k]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: libxerces-c3.2t64

  validating XML parser library for C++

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• sug: bash-completion

  programmerbar komplettering för bash-skalet

• sug: hhsuite

  sensitive protein sequence searching based on HMM-HMM alignment

• sug: hmmer

  profile hidden Markov models for protein sequence analysis

Hämta freecontact

Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Version	Paketstorlek	Installerad storlek	Filer
alpha (inofficiell anpassning)	1.0.21-14	341,0 kbyte	1.963,0 kbyte	[filförteckning]
amd64	1.0.21-14	372,1 kbyte	1.786,0 kbyte	[filförteckning]
arm64	1.0.21-14	335,0 kbyte	1.826,0 kbyte	[filförteckning]
armel	1.0.21-14	321,2 kbyte	1.625,0 kbyte	[filförteckning]
armhf	1.0.21-14	325,4 kbyte	1.325,0 kbyte	[filförteckning]
hppa (inofficiell anpassning)	1.0.21-14	338,9 kbyte	1.803,0 kbyte	[filförteckning]
i386	1.0.21-14	381,4 kbyte	1.809,0 kbyte	[filförteckning]
ia64 (inofficiell anpassning)	1.0.21-13.1+b1	370,9 kbyte	2.762,0 kbyte	[filförteckning]
m68k (inofficiell anpassning)	1.0.21-14	365,9 kbyte	1.825,0 kbyte	[filförteckning]
mips64el	1.0.21-14	352,7 kbyte	2.442,0 kbyte	[filförteckning]
ppc64 (inofficiell anpassning)	1.0.21-14	362,7 kbyte	2.338,0 kbyte	[filförteckning]
ppc64el	1.0.21-14	362,5 kbyte	2.082,0 kbyte	[filförteckning]
riscv64	1.0.21-14	358,2 kbyte	1.510,0 kbyte	[filförteckning]
s390x	1.0.21-14	345,7 kbyte	1.778,0 kbyte	[filförteckning]
sh4 (inofficiell anpassning)	1.0.21-14	394,3 kbyte	1.762,0 kbyte	[filförteckning]
sparc64 (inofficiell anpassning)	1.0.21-14	304,7 kbyte	2.662,0 kbyte	[filförteckning]
x32 (inofficiell anpassning)	1.0.21-14	375,2 kbyte	1.705,0 kbyte	[filförteckning]