On Wed, Feb 16, 2011 at 8:54 PM, David Mathog <mat...@caltech.edu> wrote: > 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 >
Note you can do that with a single command line: $ transeq asis:AAAAAAAA -filter -frame 6 >asis_1 KKX >asis_2 KKX >asis_3 KK >asis_4 FF >asis_5 FFX >asis_6 FFX Note that while using 1, 2, 3 for the forward frames is well defined, there are two conventions for the reverse frame - do you start from the left or the right? First let's just do the forward frames, $ transeq asis:AAAAAAAA -filter -frame 1 >asis_1 KKX $ transeq asis:AAAAAAAA -filter -frame 2 >asis_2 KKX $ transeq asis:AAAAAAAA -filter -frame 3 >asis_3 KK Are you happy with them? Now let's do that with the reverse complement strand: $ transeq asis:TTTTTTTT -filter -frame 1 >asis_1 FFX $ transeq asis:TTTTTTTT -filter -frame 2 >asis_2 FFX $ transeq asis:TTTTTTTT -filter -frame 3 >asis_3 FF Now let's do that with the original sequence but the negative frames: $ transeq asis:AAAAAAAA -filter -frame -3 >asis_6 FFX $ transeq asis:AAAAAAAA -filter -frame -2 >asis_5 FFX $ transeq asis:AAAAAAAA -filter -frame -1 >asis_4 FF Same results - perhaps the naming isn't as you expected? Peter _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
