[Genome] parameters for blat with 25mers

[Galt Barber]

Are your 25mers from dna-space (intronless) or mrna (may have introns)?

If the former "gapless" case, then our hgBlat parameters will work
(e.g. stepSize=5 tileSize=11) with 25mers, as long as they do not lie
on over-used tiles.

If you are using command-line stand-alone blat,
what does your command-line look like?

-Galt


On Thu, 10 May 2007, Yueming Ding wrote:

> Hi Kayla,
>
> I need your help on another problem. I am using regular BLAT with 25mers to
>scan mouse genome (use default parameters). I get hits for only half of
>the query sequences. Could you please tell me how I can set some parameters
>so that I can blat with 25mers? Thanks.
>
> Yueming
>
> -----Original Message-----
> From: Kayla Smith [mailto:kayla at soe.ucsc.edu]
> Sent: Tuesday, May 08, 2007 5:16 PM
> To: Yueming Ding
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] blat
>
>
> Yueming,
>
> I've asked one of our developers about your question and here is what he
> has to say:
>
> Please see "Replicating web-based Blat percent identity and score
> calculations" http://genome.ucsc.edu/FAQ/FAQblat.html#blat4
> which has all details needed to calculate our hgBlat score.
>
> Indels and mismatches are not treated the same,
> that includes how BLAT does alignments and
> how it calculates the final score.
>
> BLAT builds the exons as alignments with
> matches/mismatches extending from the seed
> position until the alignment cannot be extended.
>
> Then the parts are chained together giving
> a final alignment that has exons and introns.  All the
> details of the score calculation are given above.
>
> In general huge introns do not carry a huge
> penalty.  It's not subtracting one for
> each base of the intron gap. It actually only
> subtracts one for the entire gap or insert.
> In general also a mismatch consumes a base from the query
> side whereas a gap does not, e.g.
>
> mismatch T/C (T in query is consumed)
> query:  ACTGACTG
> target: ACCGACTG
>
> gap example (gap on query side, nothing in query is consumed)
> query:  ACT---------GACTG
> target: ACTCGCCGGCCCGACTG
>
> Note on repeatMatches:
> Despite the documentation, the repeatMatches feature
> of the psls is basically not used, so you won't see
> anything in that column.  Instead, a match
> in a repeated area will just be a regular match.
>
> I hope this information is helpful to you.  Please don't hesitate to
> contact us again if you require further assistance.
>
> Kayla Smith
> UCSC Genome Bioinformatics Group
>
>
>
> Yueming Ding wrote:
> > Generator Microsoft Word 11 (filtered medium) Hi, is anyone able to tell me how Jim' s BLAT handles mismatch and indels? Does BLAT treat mismatch and indels equally (by assigning the same penalty scores)? Thanks.
> >
> > Yueming Ding
> > The Jackson Laboratory
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> > From - Tue
>
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>