[BiO BB] question on RNA and species signatures

Tanney, Austin austin.tanney at almacgroup.com
Thu Jul 26 10:59:05 EDT 2007


For short BLASTs, the e-vlaue is generally not that usefull. 
Often the recommended expect for short BLASTs is 1000.
In this case its % identiy and coverage you should look for.. Realistically 100% coverage should be what you expect.

-----Original Message-----
bio_bulletin_board-bounces+austin.tanney=almacgroup.com at bioinformatics.o
[mailto:bio_bulletin_board-bounces+austin.tanney=almacgroup.com at bioinfor
matics.org]On Behalf Of Mike Marchywka
Sent: 26 July 2007 15:33
To: bio_bulletin_board at bioinformatics.org
Subject: RE: [BiO BB] question on RNA and species signatures

Thanks. Nothing on the one site but ensembl has some ideas, not sure
how to interpret yet. fwiw, ncbi does have several repeats databases


and I tried against a few of these but no low-e hits.
At higher e, there were a few suggestions in human repeats:

$ blastnew -out non_dog -nuc -hits 10 -summ 3000 -db humrep -expect 100 

          Length = 4936

Score = 26.3 bits (13), Expect = 0.22
Identities = 13/13 (100%)
Strand = Plus / Minus

Query: 12   caggatccagtcc 24
Sbjct: 4369 caggatccagtcc 4357

I also ran against
some other wgs's and there are some lower e hits to cat but still
seems to be largely dog specific( matches 38/39 IIRC).


Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
404-788-1216 (C)<- leave message
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marchywka at hotmail.com

>From: "Tanney, Austin" <austin.tanney at almacgroup.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: RE: [BiO BB] question on RNA and species signatures
>Date: Thu, 26 Jul 2007 13:51:42 +0100
>Hi Mike,
>Have you tried looking at Rfam (http://www.sanger.ac.uk/Software/Rfam/)
>miRBase (http://microrna.sanger.ac.uk/sequences/) or the ensembl genome 
>browser (http://www.ensembl.org/index.html)


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