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[ Source: fasta3  ]

Paketti: fasta3 (36.3.8i.14-Nov-2020-2~0exp0simde)

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tools for searching collections of biological sequences

The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. 

 * Protein
   - Protein-protein FASTA
   - Protein-protein Smith-Waterman (ssearch)
   - Global Protein-protein (Needleman-Wunsch) (ggsearch)
   - Global/Local protein-protein (glsearch)
   - Protein-protein with unordered peptides (fasts)
   - Protein-protein with mixed peptide sequences (fastf)


 * Nucleotide
   - Nucleotide-Nucleotide (DNA/RNA fasta)
   - Ordered Nucleotides vs Nucleotide (fastm)
   - Un-ordered Nucleotides vs Nucleotide (fasts)


 * Translated
   - Translated DNA (with frameshifts, e.g. ESTs)
     vs Proteins (fastx/fasty)
   - Protein vs Translated DNA (with frameshifts)
     (tfastx/tfasty)
   - Peptides vs Translated DNA (tfasts)


 * Statistical Significance
   - Protein vs Protein shuffle (prss)
   - DNA vs DNA shuffle (prss)
   - Translated DNA vs Protein shuffle (prfx)


 * Local Duplications
   - Local Protein alignments (lalign)
   - Plot Protein alignment "dot-plot" (plalign)
   - Local DNA alignments (lalign)
   - Plot DNA alignment "dot-plot" (plalign)

This software is often used via a web service at the EBI with readily indexed reference databases at http://www.ebi.ac.uk/Tools/fasta/.

Muut pakettiin fasta3 liittyvät paketit

  • depends
  • recommends
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  • dep: libc6 (>= 2.34)
    GNU-C-kirjasto: jaetut kirjastot
    myös näennäispaketti, jonka toteuttaa libc6-udeb
  • dep: python3
    interactive high-level object-oriented language (default python3 version)
  • rec: r-base-core
    GNU R core of statistical computation and graphics system
  • sug: bedtools
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  • sug: libdbd-mysql-perl
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  • sug: libdbi-perl
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  • sug: libhtml-tableextract-perl
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  • sug: libjson-perl
    module for manipulating JSON-formatted data
  • sug: liburi-encode-perl
    Perl module to encode and decode strings to URIs
  • sug: libwww-perl
    simple and consistent interface to the world-wide web
  • sug: libxml-twig-perl
    Perl module for processing huge XML documents in tree mode
  • sug: ncbi-blast+
    next generation suite of BLAST sequence search tools
  • sug: perl
    Larry Wallin kieli tekstitiedostojen analysointia ja raportointia varten
  • sug: python3-mysqldb
    Python interface to MySQL

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