FASTA and FASTQ - Revision history

Thorsted at 00:17, 11 June 2024

2024-06-11T00:17:57Z

Thorsted at 03:24, 11 May 2024

2024-05-11T03:24:02Z

Thorsted at 02:53, 11 May 2024

2024-05-11T02:53:32Z

Dan Tobias: /* Links */

2014-10-13T13:16:01Z

‎Links

Dan Tobias: 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}},..."

2014-04-06T04:34:50Z

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}},..."

New page

{{FormatInfo
|subcat=Scientific Data formats
|extensions={{ext|fasta}}, {{ext|fas}}, {{ext|fa}}, {{ext|seq}}, {{ext|fsa}}, {{ext|fna}}, {{ext|ffn}}, {{ext|faa}}, {{ext|mpfa}}, {{ext|frn}}, {{ext|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 ==
* [[Wikipedia:FASTA format|Wikipedia: FASTA]]
* [[Wikipedia:FASTQ format|Wikipedia: FASTQ]]
* [http://zhanglab.ccmb.med.umich.edu/FASTA/ What is FASTA format?]
* [http://www.ncbi.nlm.nih.gov/staff/tao/tools/tool_lettercode.html Single letter codes for nucleotides]
* [http://qiime.org/tutorials/processing_illumina_data.html#fastq-format Processing Illumina data: FASTQ format]
* [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]

← Older revision		Revision as of 00:17, 11 June 2024
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	Files may also be distributed in compressed forms, adding second extensions such as .fastq.gz.		Files may also be distributed in compressed forms, adding second extensions such as .fastq.gz.
		+
		+	== Samples ==
		+	* [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/ Human Genome in FASTA and other formats]
		+	* [https://github.com/hartwigmedical/testdata FASTQ File Samples]

	== Links ==		== Links ==

← Older revision		Revision as of 13:16, 13 October 2014
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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])

@@ Line 2: / Line 2: @@
 |subcat=Scientific Data formats
 |extensions={{ext|fasta}}, {{ext|fas}}, {{ext|fa}}, {{ext|seq}}, {{ext|fsa}}, {{ext|fna}}, {{ext|ffn}}, {{ext|faa}}, {{ext|mpfa}}, {{ext|frn}}, {{ext|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.

@@ Line 14: / Line 14: @@
 * .mpfa: FASTA amino acides in multiple proteins
 * .frn: FASTA non-coding RNA
-* .fastq: FASTQ
+* .fastq, .fq: FASTQ
 Files may also be distributed in compressed forms, adding second extensions such as .fastq.gz.