[Genome] blat

[Brooke Rhead]

Hello Omer,

The databases used for BLAT do not need to be formatted with NCBI's  
formatdb.

Here is a link to several frequently asked questions about BLAT,  
including advice on replicating web-based BLAT results at the command  
line:

http://genome.ucsc.edu/FAQ/FAQblat

You may also find this page, the BLAT specifications and User Guide,  
helpful:

http://genome.ucsc.edu/goldenPath/help/blatSpec.html

Please contact us again if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



On Jan 28, 2007, at 3:04 AM, omer haber wrote:

> hello,
> I tried to install blat on my linux ( I useing fedura core2 and I  
> downloaded linuxReadhat7.3) ,
> I opened the zip file , downloaded the formated databases and  
> formated it with formatdb from ncbi ( formatdb -i ciona_mrna.fasta - 
> p F -o).
> but when run a query ( blat -t=dna -q=rna ciona_mrna.fasta Iputfile  
> Outfile ) , the output that I get, is just the title
> (match   mis-    rep.    N's     Q gap   Q gap   T gap   T gap    
> strand .....).
>
> I know that it's need to give me an alignment, because when I run  
> it on the web and got good results.
>
> can you help me pleace, what I need to do to get the same results  
> as I got on the web ?
>
> thanks,
>
> Omer
>
>
>
>
>
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