Test case fasta file >8Achars AAAAAAAA all 6 frames for transeq, standard mode emits: >_1 KKX >_2 KKX >_3 KK >_4 FF >_5 FFX >_6 FFX
But... AAAAAAAA Forward TTTTTTTT Reverse abc cba <--- codons in diagram ^a^^b^^c^ phase 1 1 KKX 4 XFF x^a^^b^^c^ phase 2 2 KKX 5 XFF xx^a^^b^ phase 3 3 KK 6 FF That is, frames 4->6 are supposed to use, respectively, the same set of codons as 1->3, but translate on the opposite strand, shouldn't the number of residues returned be like in the table above, also with the X at the beginning rather than the end? Or to put it another way, shouldn't the little "x" bases be ignored on the - strand if they were also ignored on the +? Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss