I was assigned to associate a bunch of Stickleback (a fish) ESTs
to genes of other organisms (fugu, mouse, human). I downloaded the
0. My Stickleback ESTs
1. Fugu transcriptome sequences (JGI)
2. Fugu protein sequences (JGI)
3. Full-length cDNA sequences of mouse (MGC)
4. Full-length cDNA sequences of human (MGC).
One approach is to use blastx to blast 0,1,3,4 against 2. Then I
will associate any the sequences of 0,1,3,4 to the fugu protein if the
p-value < 10^-6 and identity% of the alignment >=70% (I stole these
cutoff from NCBI UniGene). Using their link to fugu protein, I can
associate my ESTs to fugu, human and mouse.
The other approach is to use tblastx to blast 0 against 1,3,4.
Using the same cutoff, I can associate my ESTs with cDNAs of other
Which approach is better? Are both approachs "legit"? Are there
better approach of this problem?
Thanks in advance.