[BiO BB] Re: A tool for gene identification

[Daniel Harari]

Dear Mahmoud,

A BlastN search of your sequence against the NCBI NR database provides rather compelling evidence that the DNA that you have cloned is bacterial in origin and unlikely to be human.  Is it possible that your PCR reaction pulled out bacterial DNA accidentally?  Perhaps you should repeat your PCR experiments using blank controls or using non human tissues / cell lines (e.g. mouse) and using the same solutions as you have to perform your earlier experiments.  If you get the same sequence using your negative controls as in your human tissue samples, then this will verify that you have an artifact here.  (I hope for you that I am wrong).

Regards,

Daniel

----- Original Message -----
From: Mhmoud Elhefnawi <mahef111 at link.net>
Date: Wednesday, May 3, 2006 23:11
Subject: [BiO BB] Re: A tool for gene identification
To: bio_bulletin_board at bioinformatics.org

> dear all,
> I thank so much all those who sent me their feedback and suggestions.
> I actually tried the Trace search, and BLAST on the  human 
> genome.Both yielded no significant similarity for humans.
> We previously submitted this sequence to Genbank   
> accession number AY083907..  It is 91% similar to an gene 
> in Eschorchia Coli...It is a /note="delta 2-isopentenyl 
> adenosine tRNA-like protein;
> possible member of the mevalonate pathway; down-regulated
> in several human tumors including liver, urinary tract,
> bladder, and submaxillary carcinoma; similar to
> Escherichia coli and Shigella flexneri delta-2 isopentenyl
> pyrophosphate transferases".
> We were able to isolate it from different human cell lines.. and 
> also from Differential display analysis on different cancers 
> like urethral cancer... what is the probability that it is a 
> novel gene not yet discovered at all, ?  and what percent 
> of the human genome is still not sequenced in order to be able 
> to search against?
> Thanks alot again for all your kind assistance,
> Mahmoud ‎
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