Package: fasta3 (36.3.8i.14-Nov-2020-3) [debports]

[ Source:  ]

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)

  Libreria C GNU: librerie condivise
  also a virtual package provided by libc6-udeb

• dep: python3

  linguaggio interattivo di alto livello orientato agli oggetti (versione python3 predefinita)

• rec: r-base-core

  nocciolo del sistema per calcoli e grafici statistici GNU R

• sug: bedtools

  suite di utilità per confrontare tratti genomici

• sug: libdbd-mysql-perl

  Interfaccia Perl5 per database MariaDB/MySQL

• sug: libdbi-perl

  Perl Database Interface (DBI)

• sug: libhtml-tableextract-perl

  modulo per estrarre il contenuto presente in tabelle HTML

• sug: libjson-perl

  modulo per manipolare dati in formato JSON

• sug: liburi-encode-perl

  modulo Perl per codificare e decodificare stringhe in URI

• sug: libwww-perl

  interfaccia semplice e coerente al world-wide web

• sug: libxml-twig-perl

  modulo Perl per processare enormi documenti XML in modalità ad albero

• sug: ncbi-blast+

  suite di prossima generazione degli strumenti di ricerca di sequenze BLAST

• sug: perl

  "Practical Extraction and Report Language" di Larry Wall

• sug: python3-mysql.connector

  implementazione in Python puro del protocollo client/server di MySQL (Python 3)

• sug: python3-mysqldb

  interfaccia Python per MySQL

• sug: python3-requests

  semplice ed elegante libreria HTTP per Python 3, fatta per esseri umani

Download fasta3

Download for all available architectures

Architecture	Package Size	Installed Size	Files
hppa (unofficial port)	907.4 kB	6,464.0 kB	[list of files]