[BiO BB] Gene Search in Worm

[Christopher Moy]

Hello,

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.

Chris