I would like to add the CDS feature to my Gff3 file, that has exons in it. I saw that genometools can do this for you
gt cds -startcodon -finalstopcodon -seqfile foo.fasta -o foo.gff3 [GFF3-FILE]
I am looking for the CDS to be the longest ORF with an ATG start codon per mRNA. Will the above command give me that? Secondly I did not see a flag for specifying the genetic code. Is this by default "standard vertebrate"?
Thanks for the help Abhijit