Fasta format - Revision history

WikiBot: Automatic synchronization with BioUML

2014-01-13T04:20:04Z

Automatic synchronization with BioUML

WikiBot: {{Type link}} used

2013-05-17T09:39:11Z

{{Type link}} used

WikiBot: Target element type added

2013-05-16T06:47:07Z

Target element type added

WikiBot: Plugin link added

2013-05-07T07:12:56Z

Plugin link added

WikiBot: Protected "Fasta format": Autogenerated page (‎[edit=sysop] (indefinite))

2013-04-04T09:28:19Z

Protected "Fasta format": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Added 'Autogenerated pages' category

2013-04-04T09:28:19Z

Added 'Autogenerated pages' category

WikiBot: Automatic synchronization with BioUML

2013-04-04T08:24:44Z

Automatic synchronization with BioUML

New page

=== FASTA format ===

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data, which usually do not exceed 80 characters. The header line begins with ">" (greater-than) symbol and gives a name and comments for the sequence. Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in amino acid sequences, U and * are acceptable letters. Numerical digits are not allowed.

==== The supported nucleic acid codes ====

A → adenosine M → A C (amino)
C → cytidine S → G C (strong)
G → guanine W → A T (weak)
T → thymidine B → G T C
U → uridine D → G A T
R → G A (purine) H → A C T
Y → T C (pyrimidine) V → G C A
K → G T (keto) N → A G C T (any)
- → gap of indeterminate length
==== The supported codes (24 amino acids and 3 special codes) ====

A alanine P proline
B aspartate or asparagine Q glutamine
C cystine R arginine
D aspartate S serine
E glutamate T threonine
F phenylalanine U selenocysteine
G glycine V valine
H histidine W tryptophan
I isoleucine Y tyrosine
K lysine Z glutamate or glutamine
L leucine X any
M methionine * translation stop
N asparagine - gap of indeterminate length
==== Example ====

>gi<nowiki>|</nowiki>5524211<nowiki>|</nowiki>gb<nowiki>|</nowiki>AAD44166.1<nowiki>|</nowiki> cytochrome b
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
==== References ====

# [http://en.wikipedia.org/wiki/FASTA_format http://en.wikipedia.org/wiki/FASTA_format]

[[Category:File formats]]

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 :Fasta format (*.fasta)
 ;Element type
-:{{Type link|track}}
+:{{Type link|collection of sequences}}
 ;Plugin
 :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

@@ Line 2: / Line 2: @@
 :Fasta format (*.fasta)
 ;Element type
-:[[File:Type-track-icon.png]] [[Track (element type)|track]]
+:{{Type link|track}}
 ;Plugin
 :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

@@ Line 1: / Line 1: @@
 ;File format title
 :Fasta format (*.fasta)
 ;Plugin
 :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

← Older revision		Revision as of 07:12, 7 May 2013
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		+	;File format title
		+	:Fasta format (*.fasta)
		+	;Plugin
		+	:[[Ru.biosoft.bsa (plugin)\|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
		+
	=== FASTA format ===		=== FASTA format ===

← Older revision		Revision as of 09:28, 4 April 2013
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	[[Category:File formats]]		[[Category:File formats]]
		+	[[Category:Autogenerated pages]]