frameshift?

Anders Gorm Pedersen gorm at cbs.dtu.dk
Wed Jul 11 12:21:37 EST 2001


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





More information about the Bio-soft mailing list