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

Hi folks,

    I was assigned to associate a bunch of Stickleback (a fish) ESTs
to genes of other organisms (fugu, mouse, human). I downloaded the
following dataset

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.
Yee Man

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