Пакунок: fasta3 (36.3.8i.14-Nov-2020-3)

[ Source: fasta3  ]

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/.

Інші пакунки пов'язані з fasta3

• dep: libc6 (>= 2.34)

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  also a virtual package provided by libc6-udeb

• dep: python3

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• rec: r-base-core

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• 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

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• sug: liburi-encode-perl

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• sug: libwww-perl

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• 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

  Мова Практичного Видобування та Побудування Звітів Лари Уолла (Larry Wall)

• sug: python3-mysql.connector

  pure Python implementation of MySQL Client/Server protocol (Python3)

• sug: python3-mysqldb

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• sug: python3-requests

  elegant and simple HTTP library for Python3, built for human beings

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