On Jan 4 2006, Alex Golubev wrote:
Hi,
I'm trying to align amino acids to nucleic acids. I'm using gapped
sequences both for the protein and for the DNA. I have several problems
and I would very appreciate if someone could help. 1. How can I parse DNA
nucleic acids and get codons. I would like to start with DNA that look
like this "ATGTAT" and get a protein that look like this "MY". I'm using
"Alphabet alpha = DNATools.getCodonAlphabet();" but I can't find
tokenization to parse the DNA string (does this make any sense?).
You can convert a SymbolList in the DNA alphabet into the equivalent symbol
list in the codon alphabet (DNAxDNAxDNA) by using
SymbolListViews.orderNSymbolList(...).
2. My
other problem is that there are frame shifts and my gapped DNA look
actually like this "AT-G-TAT". Is there any way to get/translate
locations from the codon symbols list to/from the DNA symbols list?
Ouch. What do you really want to do here?
Regards,
David Huen
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