Difference between revisions of "Gene Transfer Format"

Revision as of 13:47, 16 May 2013

File format title

Gene Transfer Format (*.gtf)

Element type

track

Plugin

ru.biosoft.bsa (Bio-sequences analyses plugin)

Gene transfer format

The gene transfer format (GTF) is an advanced version of GFF format which may contain any additional fields. The filename extension associated with such files is *.gtf.

The format consists of 8 required and up to 2 optional columns, separated by tabs (NOT spaces). The following characters must be escaped using URL escaping conventions (%XX hex codes):

tab
newline
carriage return
control characters

The following characters have reserved meanings and must be escaped when used in other contexts:

;  (semicolon)
=  (equals)
%  (percent)
&  (ampersand)
,  (comma)

Unescaped quotation marks, backslashes and other ad-hoc escaping conventions that have been added to the GTF format are explicitly forbidden

Note that unescaped spaces are allowed within fields, meaning that parsers must split on tabs, not spaces.

Undefined fields are replaced with the "." character.

Column 1: "seqid"

The ID of the landmark used to establish the coordinate system for the current feature. IDs may contain any characters, but must escape any characters not in the set [a-zA-Z0-9.:^*$@!+_?-|]. In particular, IDs may not contain unescaped whitespace and must not begin with an unescaped ">".

Column 2: "source"

The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature. Typically this is the name of a piece of software, such as "Genescan" or a database name, such as "Genbank." In effect, the source is used to extend the feature ontology by adding a qualifier to the type creating a new composite type that is a subclass of the type in the type column.

Column 3: "type"

The type of the feature (previously called the "method"). This is constrained to be either: (a)a term from the "lite" version of the Sequence Ontology - SOFA, a term from the full Sequence Ontology - it must be an is_a child of sequence_feature (SO:0000110) or (c) a SOFA or SO accession number. The latter alternative is distinguished using the syntax SO:000000.

Columns 4 & 5: "start" and "end"

The start and end of the feature, in 1-based integer coordinates, relative to the landmark given in column 1. Start is always less than or equal to end. For features that cross the origin of a circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes), the requirement for start to be less than or equal to end is satisfied by making end = the position of the end + the length of the landmark feature.

For zero-length features, such as insertion sites, start equals end and the implied site is to the right of the indicated base in the direction of the landmark.

Column 6: "score"

The score of the feature, a floating point number. As in earlier versions of the format, the semantics of the score are ill-defined. It is strongly recommended that E-values be used for sequence similarity features, and that P-values be used for ab initio gene prediction features.

Column 7: "strand"

The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown.

Column 8: "frame"

For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. In other words, a phase of "0" indicates that the next codon begins at the first base of the region described by the current line, a phase of "1" indicates that the next codon begins at the second base of this region, and a phase of "2" indicates that the codon begins at the third base of this region. This is NOT to be confused with the frame, which is simply start modulo 3.

For forward strand features, phase is counted from the start field. For reverse strand features, phase is counted from the end field.

The phase is REQUIRED for all CDS features.

Column 9: "attributes"

All four features have the same two mandatory attributes at the end of the record:

• gene_id value; A globally unique identifier for the genomic source of the transcript
• transcript_id value; A globally unique identifier for the predicted transcript.

These attributes are designed for handling multiple transcripts from the same genomic region. Any other attributes or comments must appear after these two and will be ignored. Attributes must end in a semicolon which must then be separated from the start of any subsequent attribute by exactly one space character (NOT a tab character). Textual attributes should be surrounded by doublequotes.

Here is an example of a gene on the negative strand. Larger coordinates are 5' of smaller coordinates. Thus, the start codon is 3 bp with largest coordinates among all those bp that fall within the CDS regions. Similarly, the stop codon is the 3 bp with coordinates just less than the smallest coordinates within the CDS regions.

AB000123    Twinscan     CDS    193817    194022    .    -    2    gene_id "AB000123.1"; transcript_id "AB00123.1.2";
AB000123    Twinscan     CDS    199645    199752    .    -    2    gene_id "AB000123.1"; transcript_id "AB00123.1.2";
AB000123    Twinscan     CDS    200369    200508    .    -    1    gene_id "AB000123.1"; transcript_id "AB00123.1.2";
AB000123    Twinscan     CDS    215991    216028    .    -    0    gene_id "AB000123.1"; transcript_id "AB00123.1.2";
AB000123    Twinscan     start_codon   216026    216028    .    -    .    gene_id    "AB000123.1"; transcript_id "AB00123.1.2";
AB000123    Twinscan     stop_codon    193814    193816    .    -    .    gene_id    "AB000123.1"; transcript_id "AB00123.1.2";

References

1. http://mblab.wustl.edu/GTF2.html