Ulrika Troedsson wrote:
> I am working with a sequence for which I don't have the first part. I am
> using BLASTX and TBLASTX and the sequence has similarities with the same
> gene in more than one reading frame. Does i t mean that my gene contains
> frameshifts? (or is it just because the genes are very conserved?)
If two DNA sequences are very similar (or identical) then the hypothetical
protein sequences from all six pairs of frames are also going to be very
similar (or identical). Presumably you can figure out which frame is
correct by finding a homologous PROTEIN sequence (BLASTX) or by looking at
stop codons?
> Is there a plant transposon database?
If by this you mean a database of transposon tagged loci, then the
Arabidopsis Transposon Insertion Database (ATI) might be useful:
http://stein.cshl.org/~x-pan/atidb/index.html
Hope this helps!
Anders
--
Anders Gorm Pedersen, Ph.D.
Center for Biological Sequence Analysis, www.cbs.dtu.dk
Technical University of Denmark
