NAME

DESCRIPTION

CATEGORY

USAGE

OPTIONS

• -h display full help message
• -help display options
• -v verbose
• -i inputfile if not specified, the standard input is used. This allows to place the command within a pipe.
• -o outputfile if not specified, the standard output is used. This allows to place the command within a pipe.
• -from input format (Supported: dnapat,ft,gft,gff3,gff)
• -to output format (Supported: dnapat,ft,gft,fasta,gff3,gff)

INPUT FORMATS

• ft: RSAT feature-map (extension .ft)
• dnapat: RSAT dna-pattern (extension .tab)
• gft: RSAT Genome features (file Feature.tab in the directory data/genomes)
• gff: General Feature Format as specified by the Sanger insitute (extension .gff) http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
• gff3: Generic feature format version 3 An adaptation of GFF by Lincoln Stein http://flybase.net/annot/gff3.html

OUTPUT FORMATS

• ft
• gff
• gff3

FORMAT DESCRIPTIONS

Feature formats are generally tab-delimited files. For historical reasons, different formats have been used at different sites. Originally, these formats were conceived to represent different types of information, and, for this reason, the contents of their column slightly differs. However, the main information is similar, and the differing columns can be easily extrapolated or skipped.

ft: RSAT feature-map
• col 1 map label (eg gene name)
• col 2 feature type
• col 3 feature identifier (ex: GATAbox, Abf1_site)
• col 4 strand (D for Direct, R for Reverse),
• col 5 feature start position
• col 6 feature end position
• col 7 (optional) description
• col 8 (optional) score
gft: RSAT Genome features (file Feature.tab in the directory data/genomes)
• col 1 id
• col 2 type
• col 3 name
• col 4 contig
• col 5 start
• col 6 end
• col 7 strand
• col 8 description
• col 9 chrom_position
• col 10 organism
gff: Sanger general feature file (extension .gff) Information: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
• col 1 seqname (contig or sequence ID)
• col 2 source
• col 3 feature (feature type)
• col 4 start
• col 5 end
• col 6 score
• col 7 strand (+, - or .)
• col 8 frame (0, 1, 2 or .)
• col 9 attribute
gff3: Generic Feature Format version 3 Information: http://flybase.net/annot/gff3.html
• col 1 seqid (contig or sequence ID)
• col 2 source
• col 3 feature type
• col 4 start
• col 5 end
• col 6 score
• col 7 strand (+, - or .)
• col 8 frame (=phase) (0, 1 or 2)
• col 9 attributes
ID: name of the feature
• Name: display name for the feature
• Alias: secondary name for the feature
• Parent: parent of the feature
• Target: target (of an alignment)
• Gap: alignment of the feature to the target
• Note: A free text note
• Dbxref: database cross reference
• Ontology_term: cross-reference to an ontology term

For information, contact