[Bioperl-l] Blast results question

[Sean Davis]

On 2/18/04 9:18 AM, "Jason Stajich" <jason at cgt.duhs.duke.edu> wrote:

> You might want to try using est2genome/sim4/spidey/exonerate on the
> region where you have your multiple hits if you care about the splice
> sites/predicting a gene structure.  use the start & end methods from a
> Search::Hit object to get the min/max location of the hits in the hit
> sequence $hit->start('hit'),$hit->end('hit'), extract this seq, and run
> one of the EST->genome aligners.  Or are you just trying to locate this
> approximate region of the genome in the first place?

You guessed it with the last question.  To clarify, what I need to do is to
determine whether there is a "best" hit against the genome.  I am interested
in hits with just a couple of mismatches or fewer, but over the entire
length of the query sequence.  Therefore, I need to know when I have a query
hitting to a piece of genomic sequence where the only discontinuity is due
to a splice site.  

> -jason
> 
> On Wed, 18 Feb 2004, Sean Davis wrote:
> 
>> I have a large number of blast results against the (human) genome.  The
>> query was a large number of oligos (from microarray) taken from various ESTs
>> or full-length transcripts.  I have many that are "broken" by splice sites
>> in the genome resulting in two different "hits" near each other.  Is there
>> someone who has code or suggestions about how to "stitch" these hits back
>> together?
>> 
>> Thanks,
>> Sean
>> 
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> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>