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FASTA and FASTQ - Just Solve the File Format Problem

FASTA and FASTQ

From Just Solve the File Format Problem
(Difference between revisions)
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(Created page with "{{FormatInfo |subcat=Scientific Data formats |extensions={{ext|fasta}}, {{ext|fas}}, {{ext|fa}}, {{ext|seq}}, {{ext|fsa}}, {{ext|fna}}, {{ext|ffn}}, {{ext|faa}}, {{ext|mpfa}},...")
 
(Links)
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* [http://qiime.org/scripts/extract_barcodes.html Format FASTQ sequences and barcode data]
 
* [http://qiime.org/scripts/extract_barcodes.html Format FASTQ sequences and barcode data]
 
* [http://www.bioinformaticsbox.com/tools/sequence_format_converter.php FASTA format converter]
 
* [http://www.bioinformaticsbox.com/tools/sequence_format_converter.php FASTA format converter]
 +
* [http://search.cpan.org/dist/BioPerl-1.6.901/Bio/SeqIO.pm Bio::SeqIO (Perl)] ([http://www.bioperl.org/wiki/Module:Bio::SeqIO more info]) (connected with [http://search.cpan.org/~cjfields/BioPerl-1.6.924/Bio/Seq.pm Bio::Seq])
 +
* [http://biopython.org/wiki/SeqIO SeqIO (Python)] (connected with [http://biopython.org/wiki/Seq Seq]) ([http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html more info])

Revision as of 13:16, 13 October 2014

File Format
Name FASTA and FASTQ
Ontology
Extension(s) .fasta, .fas, .fa, .seq, .fsa, .fna, .ffn, .faa, .mpfa, .frn, .fastq

FASTA and FASTQ are text-based formats for representing nucleotide (DNA or RNA) or peptide sequences, used in biology. The FASTA format is a simple representation of the elements of the sequences using letters (the standard C, G, T, and A for DNA nucleotides, and other letters for special uses, as well as a set of letters for peptides in amino acids), while FASTQ also encodes quality scores for the data.

File extensions

A number of extensions are used, and they are not always completely standardized.

  • .fasta, .fas, .fa, .seq, .fsa: Generic FASTA
  • .fna: FASTA nucleic acids
  • .ffn: FASTA nucleotide coding regions for a genome
  • .faa FASTA amino acids
  • .mpfa: FASTA amino acides in multiple proteins
  • .frn: FASTA non-coding RNA
  • .fastq: FASTQ

Files may also be distributed in compressed forms, adding second extensions such as .fastq.gz.

Links

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