[BiO BB] Hello need info

Iddo Friedberg idoerg at burnham.org
Mon Jan 15 16:30:29 EST 2007

pathan khan wrote:
> Hello
> I have generated a few ESTs from my experiments and have some questions to
> be addressed...I will be very happy to get suggestions and Help in this
> regard..
> 1. do contigs similar in base composition correspond to the same gene? 

If by "base composition" you mean the frequency of each base, then the 
answer is "no". If you mean base sequence, then the answer is "probably 
yes", although paralogs or low complexity sequences might give you a 
false positive.

> not what could be the possible explanation?

Explanation for what? Similar base composition? Many genes can have 
similar ATGC ratios, especially in the same organism. It doesn't really 
mean much in this context.

> 2.Why are my ESTs not showing Hits with the already deposited ESTs of the
> same organism although the protein for which they are coding are identical
> but from different organisms.

This question seems to be self contradictory. At the beginning you say 
that your ESTs are from the "same organism", but then you say that the 
"protein[s] for which they are coding" are from a different organism. 
Which is it?

In any case, many ESTs in the NCBI dbEST only partially cover an 
organism's transcriptome. So it may be that you simply cloned ESTs that 
were not deposited in NCBI.

Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
T: +1 858 646 3100 x3516

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