FASTA and FASTQ
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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
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
Categories:
- File Formats
- Electronic File Formats
- Scientific Data formats
- File formats with extension .fasta
- File formats with extension .fas
- File formats with extension .fa
- File formats with extension .seq
- File formats with extension .fsa
- File formats with extension .fna
- File formats with extension .ffn
- File formats with extension .faa
- File formats with extension .mpfa
- File formats with extension .frn
- File formats with extension .fastq
