Blast search help needed.

[Michael Perry]

ckafer at iastate.edu (Chris Kafer) wrote:

>I would like to be able to input several Kb of DNA sequence and have a
>blast search against the protein databases and the EST database on all
>ORFs over 30 amino acids long in all 3 reading frames in each
>direction.  Is there a simple way to do this?  

Chris,
Sounds like a job for blastx.  Point your browser to the NCBI BLAST
web page at http://www.ncbi.nlm.nih.gov/BLAST/ and check out the
following programs:  

blastx:  compares a nucleotide query sequence translated in all
reading frames against a protein sequence database 

tblastx: compares the six-frame translations of a nucleotide query
sequence against the six-frame translations of a nucleotide sequence
database. 

Mike