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Paketti: atac (0~20150903+r2013-3)

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atac

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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.

Muut pakettiin atac liittyvät paketit

  • depends
  • recommends
  • suggests
  • dep: gnuplot
    Command-line driven interactive plotting program.
    myös näennäispaketti, jonka toteuttaa gnuplot-nox, gnuplot-qt, gnuplot-x11
  • dep: leaff
    biological sequence library utilities and applications
  • dep: libc6 (>= 2.14)
    GNU C Library: Shared libraries
    myös näennäispaketti, jonka toteuttaa libc6-udeb
  • dep: libfile-which-perl
    Perl module for searching paths for executable programs
  • dep: libgcc1 (>= 1:3.0)
    GCC support library
  • 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)

Imuroi atac

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amd64 376.2 kt2683 kt [tiedostoluettelo]