Gene identification troubles (bit long)

Nico van Belzen belzen at hema.fgg.eur.nl
Wed Mar 4 05:18:50 EST 1998


In article <6deokn$ck5$1 at bertrand.ccs.carleton.ca>, 
tenglish at rideau.carleton.ca says...

(deletions)

>2)  What do we do with a gene that has been sequenced from start
>to finish (UTR, start codon, stop codon, poly A signal and poly A
>tail) but still shows no homology with anything in GenBank???  What
>further experiments can be done?

Have you tried BlastP/TblastN searching with the deduced protein sequence? 
More sensitive in cross-species than BlastN.

>3)  Are there other databases that are more useful to those of
>us working with invertebrates?  

specialized organism databases such as elegans, yeast, perhaps

>5)  We have tried translating the gene sequence into amino acids
>then searching the "protein" sequence for motifs (via a database).
>How reliable are the results?  How much useful information can be
>obtained this way?

E.g. Prosite NOT-frequently-occurring motifs may give clues as to 
function; however, the info will have to be confirmed by experiments IMHO.

Nico van Belzen (belzen at hema.fgg.eur.nl)




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