Here is another worked example with a small but real mRNA fragment. (Best cut and paste it into a program with a fixed width font).
Test sequence: >for (AKA gi|1728|emb|V00893.1, this is "+" direction) TCGAAAACCGGGCCATGAAGGATGAGGAGAAGATGGAGCTGCA GGAGATGCAGCTGAAGGAGGCCAAGCACATTGCCGAGGACTCA GACCGCAAATACGAGGAGGTGGCCAGGAAGCTGGTGATCCTCGA >rev (for reversed) TCGAGGATCACCAGCTTCCTGGCCACCTCCTCGTATTTGCGGT CTGAGTCCTCGGCAATGTGCTTGGCCTCCTTCAGCTGCATCTC CTGCAGCTCCATCTTCTCCTCATCCTTCATGGCCCGGTTTTCGA Transeq output, all 6 frames, for >for and >rev >for_1 SKTGP*RMRRRWSCRRCS*RRPSTLPRTQTANTRRWPGSW*SSX >for_2 RKPGHEG*GEDGAAGDAAEGGQAHCRGLRPQIRGGGQEAGDPR >for_3 ENRAMKDEEKMELQEMQLKEAKHIAEDSDRKYEEVARKLVILX >for_4 RGSPASWPPPRICGLSPRQCAWPPSAASPAAPSSPHPSWPGFR >for_5 SRITSFLATSSYLRSESSAMCLASFSCISCSSIFSSSFMARFSX >for_6 EDHQLPGHLLVFAV*VLGNVLGLLQLHLLQLHLLLILHGPVFX >rev_1 SRITSFLATSSYLRSESSAMCLASFSCISCSSIFSSSFMARFSX >rev_2 RGSPASWPPPRICGLSPRQCAWPPSAASPAAPSSPHPSWPGFR >rev_3 EDHQLPGHLLVFAV*VLGNVLGLLQLHLLQLHLLLILHGPVFX >rev_4 RKPGHEG*GEDGAAGDAAEGGQAHCRGLRPQIRGGGQEAGDPR >rev_5 SKTGP*RMRRRWSCRRCS*RRPSTLPRTQTANTRRWPGSW*SSX >rev_6 ENRAMKDEEKMELQEMQLKEAKHIAEDSDRKYEEVARKLVILX Output from a different program, all 12 frame options shown on the fasta header line as: phase(strand) Positive phases are measured from sequence position 1. Negative phases measured from sequence position N, the last base in the sequence. This program differs from transeq in that any partial codon is emitted as an X. Note how transeq output never starts with an X, whereas here the X maintains its position on the Nucleic acid sequence, for instance, +1(+) and +1(-). >gi|1728|emb|V00893.1|[+1(+)] SKTGP*RMRRRWSCRRCS*RRPSTLPRTQTANTRRWPGSW*SSX >gi|1728|emb|V00893.1|[+2(+)] RKPGHEG*GEDGAAGDAAEGGQAHCRGLRPQIRGGGQEAGDPR >gi|1728|emb|V00893.1|[+3(+)] ENRAMKDEEKMELQEMQLKEAKHIAEDSDRKYEEVARKLVILX >gi|1728|emb|V00893.1|[+1(-)] XRGSPASWPPPRICGLSPRQCAWPPSAASPAAPSSPHPSWPGFR >gi|1728|emb|V00893.1|[+2(-)] SRITSFLATSSYLRSESSAMCLASFSCISCSSIFSSSFMARFS >gi|1728|emb|V00893.1|[+3(-)] XEDHQLPGHLLVFAV*VLGNVLGLLQLHLLQLHLLLILHGPVF >gi|1728|emb|V00893.1|[-1(-)] SRITSFLATSSYLRSESSAMCLASFSCISCSSIFSSSFMARFSX >gi|1728|emb|V00893.1|[-2(-)] RGSPASWPPPRICGLSPRQCAWPPSAASPAAPSSPHPSWPGFR >gi|1728|emb|V00893.1|[-3(-)] EDHQLPGHLLVFAV*VLGNVLGLLQLHLLQLHLLLILHGPVFX >gi|1728|emb|V00893.1|[-1(+)] XRKPGHEG*GEDGAAGDAAEGGQAHCRGLRPQIRGGGQEAGDPR >gi|1728|emb|V00893.1|[-2(+)] SKTGP*RMRRRWSCRRCS*RRPSTLPRTQTANTRRWPGSW*SS >gi|1728|emb|V00893.1|[-3(+)] XENRAMKDEEKMELQEMQLKEAKHIAEDSDRKYEEVARKLVIL >gi|1728|emb|V00893.1| Regards, David Mathog [email protected] Manager, Sequence Analysis Facility, Biology Division, Caltech _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
