[BiO BB] Gene Search in Worm

[hararid at bgumail.bgu.ac.il]

Chris,

It is possible that your worm gene does not have homologues in higher organisms, although it is likely that you will find homologs amongst different worm species.  Many such examples exist.  The same goes for flies, etc.

The most sensitive search that you can perform in which to hunt for homologs is to perform the following:  Extract the homologs from different worm species.  Create a multiple sequence alignment (E.g. ClustalW).  Then use the multiple sequence alignment to generate a PROFILE.   You can then run this profile againt various databases (IE: profilesearches).  This can be done using the HMMER algorithm or using a Smith-Waterman based profilesearch algorithm. For the latter I refer you to this site:
http://eta.embl-heidelberg.de:8000/misc/

Daniel

hararid at bgu.ac.il


> 
> From: Christopher Moy <moyc at mail.med.upenn.edu>
> Date: 2006/02/19 א PM 08:51:15 GMT+02:00
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] Gene Search in Worm
> 
> 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
> 
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