|Modifiers for FASTA Definition Lines|
Source information contained within FASTA definition lines can be automatically fielded to the appropriate feature or descriptor using Sequin or tbl2asn. Listed below are the currently available modifiers. You may include as many modifiers as you like, but each must be bounded by a set of brackets. The name of the modifier must be written exactly as shown in the list below. An example of a string of modifiers is
[organism=Mus musculus] [strain=BALB/c] [chromosome=5] [sex=male] [tissue-type=testis] [moltype=mRNA]
Do not use hard returns between the bracketed data. The FASTA definition line must be a single line of text and can not contain a hard return. If you have trouble importing your FASTA sequences, please confirm that a hard return was not inserted by your editing software.
Descriptions of these modifiers can be found in the Sequin help documentation. These source modifiers should be used in the format
Culture-collection has a mandatory format of "institution code:collection code:culture_id". However, collection code is not required. Specimen-voucher and bio-material have optional structured formats.
Other modifiers do not include any submitter provided text. The format for these modifiers in the FASTA definition line is
[modifier= ] or [modifier=TRUE]
Modifiers using this format are
environmental-sample germline metagenomic rearranged transgenic
Many of the descriptors that refer to the molecule sequenced and the genetic code can be edited using the FASTA definition line. In all cases, these descriptors have a controlled vocabulary and should only be added when their values differ from the default value.
[gcode=1] or [mgcode=5]
would set the nuclear genetic code to "The Standard Code" (translation table 1) or the mitochondrial genetic code to "The Invertebrate Mitochondrial Code" (translation table 5).
Questions or Comments?
Write to the NCBI Service Desk
Revised December 2, 2013.