Pakket: atac (0~20150903+r2013-9 en anderen)

[ Bron: kmer  ]

genome assembly-to-assembly comparison

atac computes a one-to-one pairwise alignment of large DNA sequences. It first finds the unique k-mers in each sequence, chains them to larger blocks, and fills in spaces between blocks. It was written primarily to transfer annotations between different assemblies of the human genome.

The output is a set of ungapped 'matches', and a set of gapped 'runs' formed from the matches. Each match or run associates one sequence with the other sequence. The association is 'unique', in that there is no other (sizeable) associations for either sequence. Thus, large repeats and duplications are not present in the output - they appear as unmapped regions.

Though the output is always pairwise, atac can cache intermediate results to speed a comparisons of multiple sequences.

This package is part of the Kmer suite.

Andere aan atac gerelateerde pakketten

• dep: gnuplot

  Command-line driven interactive plotting program.
  Ook een virtueel pakket geboden door: gnuplot-nox, gnuplot-qt, gnuplot-x11

• dep: leaff

  biological sequence library utilities and applications

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

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

  dep: libc6 (>= 2.39) [sh4]

• dep: libc6.1 (>= 2.36) [ia64]

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6.1-udeb

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

• dep: libfile-which-perl

  Perl module for searching paths for executable programs

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

  GCC support bibliotheek

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

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

  dep: libgcc-s1 (>= 4.2) [i386, ia64, sh4]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support bibliotheek

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support bibliotheek

• dep: libstdc++6 (>= 5.2)

  GNU Standard C++ Library v3

• dep: libunwind8 [ia64]

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

• dep: meryl

  in- and out-of-core kmer counting and utilities

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: python3

  interactive high-level object-oriented language (default python3 version)

  dep: python3 (<< 3.12) [ia64]

  dep: python3 (<< 3.13) [niet ia64]

  dep: python3 (>= 3.11~) [ia64]

  dep: python3 (>= 3.12~) [niet ia64]

• dep: python3.11 [ia64]

  Interactive high-level object-oriented language (version 3.11)

• dep: python3.12 [niet ia64]

  Interactive high-level object-oriented language (version 3.12)

• rec: kmer-examples

  sample data for kmer suite of tools for DNA sequence analysis

atac downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
alpha (unofficial port)	0~20150903+r2013-9	395,7 kB	3.503,0 kB	[overzicht]
amd64	0~20150903+r2013-9	377,4 kB	2.788,0 kB	[overzicht]
arm64	0~20150903+r2013-9	357,5 kB	3.360,0 kB	[overzicht]
armel	0~20150903+r2013-9	349,3 kB	2.514,0 kB	[overzicht]
armhf	0~20150903+r2013-9	345,0 kB	2.102,0 kB	[overzicht]
hppa (unofficial port)	0~20150903+r2013-9	463,8 kB	3.011,0 kB	[overzicht]
i386	0~20150903+r2013-9	401,8 kB	2.994,0 kB	[overzicht]
ia64 (unofficial port)	0~20150903+r2013-8+b3	511,8 kB	4.444,0 kB	[overzicht]
m68k (unofficial port)	0~20150903+r2013-9	406,3 kB	2.906,0 kB	[overzicht]
mips64el	0~20150903+r2013-9	389,9 kB	3.663,0 kB	[overzicht]
ppc64 (unofficial port)	0~20150903+r2013-9	393,2 kB	3.808,0 kB	[overzicht]
ppc64el	0~20150903+r2013-9	405,5 kB	3.808,0 kB	[overzicht]
riscv64	0~20150903+r2013-9	406,7 kB	2.460,0 kB	[overzicht]
s390x	0~20150903+r2013-9	340,5 kB	2.739,0 kB	[overzicht]
sh4 (unofficial port)	0~20150903+r2013-9	456,1 kB	3.402,0 kB	[overzicht]
sparc64 (unofficial port)	0~20150903+r2013-9	358,2 kB	23.361,0 kB	[overzicht]
x32 (unofficial port)	0~20150903+r2013-9	383,5 kB	2.730,0 kB	[overzicht]