What now???

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Tue Aug 29 06:09:57 EST 1995


> From: lowry at russell.ucsf.edu.ucsf.edu (Dorothy Lowry)
> Subject: What now???

> We have a clone.  We suspect that it codes for something
> because it is derived from mRNA (a cDNA clone, naturally).
> We made a blast search against the nr database of DNA, and
> also against the nr database of proteins and didn't come 
> up with ANYTHING except a couple of EST's about which
> nothing is known yet.
> 
> We translated it in all 4 reading frames and scanned it
> against prosite - no motifs found.  In any of the 6.
> 
> We used codonpreference in GCG to plot the codon preference.
> It isn't REALLY strong, but it isn't too bad for the ORF
> we suspect to code for the protein.
> 
> Does anyone have any suggestions about where to go from 
> here?  

Dear Chie,

1) what is the EST accession number? What organism?

look it up in dbEST, you may have more information there.

for dbEST, look at either the dbEST retrieve server

send:

datalib dbest   
help

in body of message to:      

retrieve at ncbi.nlm.nih.gov

Or look it up at:

http://www.ncbi.nlm.nih.gov/dbEST/

2) How much more work do you want to do?  From the above you may 
   get the information to get the plasmid, which you may want to 
   completly sequence.  

3) did you do a tblastx with your nucleotide sequence vs the dbEST
   database?  That may produce some more candidate ESTs, and it is 
   a much better way of checking for similarities to ESTs.

Not quite sure what you are going after?

> Thanks in advance,
> Chie Sakanaka
>
> PS.  Please respond to chies at itsa.ucsf.edu (this is someone
> else's account and I cannot read e-mail here!).
> ============================================================================
> Dorothy Lowry                                     email:  lowry at cgl.ucsf.edu

Also check with Dorothy ... she was asking me this very question yesterday ...

regards,

francis

--
| B.F. Francis Ouellette  
| GenBank
|
| francis at ncbi.nlm.nih.gov   




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