Gene Transfer Format
- File format title
- Gene Transfer Format (*.gtf)
- Element type
- 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";