Aims and general description#

ORFtrack scans a given genome in the six frames, and searches for all possible ORFs longer than a given size (default: 60 nucleotides - STOP codons excluded). It annotates them according to a set of genomic features (e.g. noncoding intergenic, coding, noncoding and overlapping with a specific genomic feature - see the ORF annotation section for more details). ORFtrack takes as inputs a fasta file containing the nucleotide sequences of all chromosomes or contigs and their corresponding annotations in a gff file. The program returns a new gff file that contains all identified ORFs. In addition, the amino acid sequences of all annotated ORFs or specific subsets of ORFs (i.e. only noncoding intergenic ORFs for example) can be extracted and written in a fasta file with ORFget, a tool provided with ORFtrack.