What I want to do is say something like in sequence D translate region 1-100 in frame 1 from 102-150 in frame 3 from 160-180 frame -3
I would typically extract this information from a blastx table and (the idea I had) feed it into EMBOSS's transeq... However transeq seems to mess up which frame does what, and even in the help it says (for the -region function) :
"Note: you should not try to use this option with any other frame than the default, -frame=1"
I wonder if there is any software that can do this? I've looked at bioperl, and haven't seen anything that caught my eye .... ? thoughts?
I get the correct frames from parsing my blastx output by printing out $hsp->hitstring or $hsp->querystring.thats not the issue what I would like is to adjust that information from the blast output so that instead of getting 5 or 6 fragments of the protein I get a single string that is correct for the protein in the several frames blastx has detected. I thought I could do this with transec, but for any given information in the blast table it shows a different result to the transec output (I've also corrected the GFF frame() used in SearchIO to show the blastX frame).Is blast skipping bases?
Also it doesn't allow multiple commands
I think your probably right about transeq though... too much "intuition"
I would not use the BLAST output for this task. Since BLAST tells you the frames, why not just go back to the original input sequence? As your question says: "How do I translate different regions of my sequence in different frames."