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[ Zdroj: kmer  ]

Balík: atac (0~20150903+r2013-3)

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.

Ostatné balíky súvisiace s balíkom atac

  • závisí
  • odporúča
  • navrhuje
  • dep: gnuplot
    Command-line driven interactive plotting program.
    tiež virtuálny balík poskytovaný balíkom gnuplot-nox, gnuplot-qt, gnuplot-x11
  • dep: leaff
    biological sequence library utilities and applications
  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    tiež virtuálny balík poskytovaný balíkom libc6-udeb
    dep: libc6 (>= 2.7) [i386]
  • dep: libfile-which-perl
    Perl module for searching paths for executable programs
  • dep: libgcc1 (>= 1:3.0) [amd64]
    GCC support library
    dep: libgcc1 (>= 1:4.2) [i386]
  • dep: libstdc++6 (>= 5.2)
    GNU Standard C++ Library v3
  • dep: meryl
    in- and out-of-core kmer counting and utilities
  • dep: perl
    Larry Wall's Practical Extraction and Report Language
  • dep: python
    interactive high-level object-oriented language (default version)
  • dep: python2.7
    Interactive high-level object-oriented language (version 2.7)

Stiahnuť atac

Stiahnuť pre všetky dostupné architektúry
Architektúra Veľkosť balíka Nainštalovaná veľkosť Súbory
amd64 376.2 kB2683 kB [zoznam súborov]
i386 417.3 kB3073 kB [zoznam súborov]