[BiO BB] Gene Search in Worm
moyc at mail.med.upenn.edu
Sun Feb 19 13:51:15 EST 2006
I have been trying to find a gene in worm that has orthologs in higher
order taxa (human, chimp, dog, etc) and in fungi (yeast, candid
albicans, etc). Using the protein database from wormbase I have ran
HMM, PSI-BLAST, FuzzPro, MEME and BLOCKS to find a similar domain
structure shared among all homologs. Although I find some loose
e-values (.001-.1) but the proteins that have this score fail to
contain distinct domains that is shared among all putative orthologs.
From what I can tell, it is possible that there are no proteins in the
current wormpep database. I have also performed tblastn runs using
various orthologs as queries to search for genome wide hits to the worm
but any prospective ortholog fails to contain the domains in other
orthologs. Does anyone have any other suggestions for further
searching? Should I consider a more comprehensive sequence alignment
strategy (Smith Waterman,etc).
Note: There is no putative structure for this gene available right now.
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