Editing FASTA format (section)

==Sequence representation==

Following the header line, the actual sequence is represented. Sequences may be [[primary structure|protein sequences]] or [[nucleic acid]] sequences, and they can contain gaps or alignment characters (see [[sequence alignment]]). Sequences are expected to be represented in the standard [[International Union of Biochemistry and Molecular Biology|IUB]]/[[International Union of Pure and Applied Chemistry|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 character; and in amino acid sequences, U and * are acceptable letters (see below). Numerical digits are not allowed but are used in some databases to indicate the position in the sequence. The nucleic acid codes supported are:<ref>
{{cite web |author=Tao Tao |date=2011-08-24 |title=Single Letter Codes for Nucleotides |url=https://www.ncbi.nlm.nih.gov/staff/tao/tools/tool_lettercode.html |url-status=dead |archive-url=https://web.archive.org/web/20120914234405/http://www.ncbi.nlm.nih.gov/staff/tao/tools/tool_lettercode.html |archive-date=2012-09-14 |access-date=2012-03-15 |work=[NCBI Learning Center] |publisher=[[National Center for Biotechnology Information]]}}</ref><ref>{{cite web |url=http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html |title=IUPAC code table |publisher=NIAS DNA Bank |url-status=dead |archive-url=https://web.archive.org/web/20110811073845/http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html |archive-date=2011-08-11 }}</ref><ref>{{cite web |title=anysymbol |url=https://mafft.cbrc.jp/alignment/software/anysymbol.html |website=MAFFT - a multiple sequence alignment program}}</ref>
{| class="wikitable sortable" style="border:solid 1px black;"
! Nucleic Acid Code
! Meaning
! Mnemonic
|-
| A
| A
| [[adenine|'''A'''denine]]
|-
| C
| C
| [[cytosine|'''C'''ytosine]]
|-
| G
| G
| [[guanine|'''G'''uanine]]
|-
| T
| T
| [[thymine|'''T'''hymine]]
|-
| U
| U
| [[uracil|'''U'''racil]]
|-
| (i)
| i
| [[inosine|'''i'''nosine]] (non-standard)
|-
| R
| A or G (I)
| [[purine|pu'''R'''ine]]
|-
| Y
| C, T or U
| [[pyrimidine|p'''Y'''rimidines]]
|-
| K
| G, T or U
| bases which are [[ketone|'''K'''etones]]
|-
| M
| A or C
| bases with [[amino|a'''M'''ino groups]]
|-
| S
| C or G
| '''S'''trong interaction
|-
| W
| A, T or U
| '''W'''eak interaction
|-
| B
| not A (i.e. C, G, T or U)
| '''B''' comes after A
|-
| D
| not C (i.e. A, G, T or U)
| '''D''' comes after C
|-
| H
| not G (i.e., A, C, T or U)
| '''H''' comes after G
|-
| V
| neither T nor U (i.e. A, C or G)
| '''V''' comes after U
|-
| N
| A C G T U
| '''N'''ucleic acid
|-
| -
| gap of indeterminate length
|
|}

The amino acid codes supported (22 amino acids and 3 special codes) are:
{| class="wikitable sortable" style="border:solid 1px black;"
! Amino Acid Code
! Meaning
|-
| A
| [[Alanine]]
|-
| B
| [[Aspartic acid]] (D) or [[Asparagine]] (N)
|-
| C
| [[Cysteine]]
|-
| D
| [[Aspartic acid]]
|-
| E
| [[Glutamic acid]]
|-
| F
| [[Phenylalanine]]
|-
| G
| [[Glycine]]
|-
| H
| [[Histidine]]
|-
| I
| [[Isoleucine]]
|-
| J
| [[Leucine]] (L) or [[Isoleucine]] (I)
|-
| K
| [[Lysine]]
|-
| L
| [[Leucine]]
|-
| M
| [[Methionine]]/[[Start codon]]
|-
| N
| [[Asparagine]]
|-
| O
| [[Pyrrolysine]] (rare)
|-
| P
| [[Proline]]
|-
| Q
| [[Glutamine]]
|-
| R
| [[Arginine]]
|-
| S
| [[Serine]]
|-
| T
| [[Threonine]]
|-
| U
| [[Selenocysteine]] (rare)
|-
| V
| [[Valine]]
|-
| W
| [[Tryptophan]]
|-
| Y
| [[Tyrosine]]
|-
| Z
| [[Glutamic acid]] (E) or [[Glutamine]] (Q)
|-
| X
| any
|-
| *
| translation stop
|-
| -
| gap of indeterminate length
|}