Package: fasta3 (36.3.8i.14-Nov-2020-1)

[ 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/.

Other Packages Related to fasta3

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  also a virtual package provided by 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

  suite of utilities for comparing genomic features

• sug: libdbd-mysql-perl

  Perl5 database interface to the MariaDB/MySQL database

• sug: libdbi-perl

  Perl Database Interface (DBI)

• sug: libhtml-tableextract-perl

  module for extracting the content contained in HTML tables

• 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 Wall's Practical Extraction and Report Language

• sug: python3-mysqldb

  Python interface to MySQL

Download fasta3

Download for all available architectures

Architecture	Package Size	Installed Size	Files
amd64	902.2 kB	6,970.0 kB	[list of files]
arm64	805.2 kB	6,702.0 kB	[list of files]
armel	807.9 kB	6,924.0 kB	[list of files]
armhf	771.9 kB	5,324.0 kB	[list of files]
i386	853.3 kB	6,924.0 kB	[list of files]
mips64el	809.3 kB	6,742.0 kB	[list of files]
mipsel	801.6 kB	6,609.0 kB	[list of files]
ppc64el	884.6 kB	8,238.0 kB	[list of files]
s390x	826.1 kB	6,836.0 kB	[list of files]