just to follow up on Duncan's post. I have a vaguely related question. I
have cloned a gene and would like to do some phylogenetic analysis of the
related sequences. I want to also include sequences pieced together from
EST's and from the different genomic sequencing projects. Just from
checking how some of these sequences match with my own, there are plenty
of sequencing errors in these sequences. Lots of insertions/deletions...
Ideally, by piecing together the info from genomic and EST sequencing
projects, I would be able to piece stuff together. But is there any easy
way to derive consensus sequences from several sequences thought to be
part of the same gene ? preferably not using some fancy shmancy program
that I can't obtain for free/small amount of cash.
The major problem is that since these sequences contain extraneous bases,
trying to come up with a "correct" consensus sequence (to then translate
in order to derive phylogenetic trees based on protein sequences) would be
relatively nightmarish. Any thoughts ?
thanks in advance,