[Genome] Blat question

[Heather Trumbower]

Hi Wes:

We are discussing your question.   Can we ask you what version of blat 
you are running?

To see the version, just type blat by itself on the command line.
The version number appears near the beginning of the usage message.

Thanks.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Mon, 20 Nov 2006, Wes Barris wrote:

> Hi,
>
> I have been using blat a lot for the past few years.  I have just encountered
> something that I have not seen before.  I am blatting a sequence against
> Btau3 BTA18 like this:
>
> blat BTA18.fa in.fa out.psl -minIdentity=90 -t=dna -q=dna -out=psl -noHead 
> -ooc=11.ooc -mask=lower -qMask=lower
>
> The psl output produced looks looks like this:
>
> 889     64      0       0       2       -110    2       633138  - 
> oacn14 843      0       843     BTA18   62891490        56102099 
> 56736190       4133,87,463,270, 0,136,223,573, 
> 56102099,56102232,56102616,56735920,
>
> When I convert this to a side-by-side alignment, it produces HSPs that 
> overlap.
> In the attached file, notice that the first HSP ends at query coordinate 270
> and that the second HSP starts at query coordinate 158.  Both HSPs are using
> an overlapping portion of the query sequence.  The target coords are from
> different areas of BTA18.
>
> In all of the blatting I have done, I have never seen this happen.  Is this
> simply a very unique case or is something wrong?
>
> I have attached both the in.fa file and the out.sbs file.
>