How can I link EST of a species to cDNAs of the other species?
Yee Man Chan
ymc at yahoo.com
Thu Feb 13 05:16:16 EST 2003
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.
More information about the Bio-soft