The Uniform Feature Object (UFO) is the standard way used on the EMBOSS command line to refer to sequence feature input and output files. In an analogous way to USAs (Section 6.6, “The Uniform Sequence Address (USA)”), the UFO specifies:
The format of the features in the file
The name of the file
The UFO has the general syntax:
|
For example:
embl:results.dat |
The permissible names for the supported feature formats (Section A.1, “Supported Sequence Formats”) are:
embl, emEMBL, GenBank and DDBJ nucleotide sequence database.
swissprot, swiss, swSWISSPROT protein database.
pir, nbrfNBRF / PIR protein database (now merged into UniProt).
gffACEDB Database General Feature Format (GFF) format.
Therefore, any of the following UFOs are valid:
embl: |
em: |
swissprot: |
swiss: |
If no format is specified, the default GFF format is assumed. You can override the default by using inbuilt command line qualifiers (Section 6.4, “Datatype-specific Command Line Qualifiers”).