[Genome] target scan results..

[Rachel Harte]

Hello Juliette,

I got input from several people in our group to help answer some of your
questions. Here are the answers:

1) The targetScan track is still available. It is not on the latest human
assembly. It is on the hg17 (May 2004) human assembly. It is called
T-ScanS miRNA and can be found in the "Expression and Regulation" group of
tracks (below the Browser image).

2) The most successful approaches for both of these tasks are comparative,
and genomic scans are often performed by the tool developers. We don't
know of any good scanning tools for single sequences. One approach that
you could try is homology searches against known miRNAs, but this would
probably not be meaningful for the (short) miRNA targets.

3) You could use the BLAT alignment program for aligning these sequences.
You can download this for local use (it is free for non-profit, academic
and personal use):

http://genome.ucsc.edu/FAQ/FAQblat#blat3

100 kb for a query sequence is about its limit. Before you try using this,
you could break your sequence up into 25 kb chunks and use our web-based
BLAT to align it to the human genome and check that you are getting
sensible results. Web-based BLAT can be found by following the BLAT link
on the top blue menu bar of the Genome Browser pages.

Another suggestion is to use the Blastz alignment program following by
chaining. This is what we use when we do alignments of one genome versus
another - see the Chain tracks in the Comparative Genomics group. Blastz
is available from Webb Miller's lab at Penn State university:

http://www.bx.psu.edu/miller_lab/

We have the programs for chaining. If Blat doesn't work well for you and
you wish to try this method, then please contact us for more information.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Tue, 12 Dec 2006, Juliette Faraco wrote:

> Hi,
> I wonder if you can help me. I am currently attempting to align
> specific MHC haplotype chunks in order to detect variations between
> specific haplotypes.  I study Narcolepsy, which is very strongly
> associated with dQB1*0602, and this most commonly occurs on a
> haplotype with DQA1*0102 and DRB1 1501.  (A number of specific
> haplotype chunks are deposited in Genbank). We know that other class
> II HLA alleles in certain haplotype contexts confer risk / or
> protection for narcolepsy, and are interested in looking carefully
> at these to see if there might be insertions or deletions leading to
> these effects.  One possibility (although remote) might be a miR
> target site etc etc.
>
> I have a few questions which I wonder if you can answer (directly
> related to browser and other...)
>
> 1- Browser related: I'm sure that previously I was able to view
> targetScan hits on your browser (nothing in my HLA region), but I
> can't even see these today. I've tried to  find this track on the
> configure page, and can't find it.  Can you please tell me how to
> bring it up?
>
> 2-not browser related: I was thinking of taking regions that are
> relative insertions/deletions between pairs of haplotypes to
> determine if any MIR related genes/targets are within. However, it
> seems that the available software is in context of searching results
> among scans that have already been done. In the case of HLA, I know
> that there are differences (insertions/deletions, sometimes 1kb+)
> between haplotypes, so I don't trust whether they are really not
> there, or whether a query with different sequence might turn up
> something positive. My question is whether there  is a software
> format where I can essentially input my genomic sequence and it will
> spit out any potential microRNAs or targets.  Are you familiar with a
> suitable way for me to do this?  I'm at Stanford, but in a very
> isolated lab, and don't know anybody doing this.
>
> 3- not browser related:  I'm doing these HLA alignments with enormous
> amounts of manual work. I'm sure there must be a more automated
> methodology! Since you are bioinformatics people, I hope you can
> answer!  My sequence analysis/ alignment program is Sequencher from
> Genecodes. Their tech support and all resources have not been able to
> help with my problem.  I am aligning ~100kb chunks of DNA from
> various haplotypes.  The software can get the alignment started, but
> once it hits a big enough insertion (gap) then it just freaks out and
> "aligns" the remainder in nonsense fashion (~ all bases mismatched).
> Then using Blast 2 results and my eyes, I  go and manually fix the
> remainder of the alignment- sometimes 30 Kb of this!  I don't know
> how else to do this, can you suggest a software that will spare my
> eyes and my time?
>
> thank you so much for any help,
> Juliette
> --
> Juliette Faraco, PhD
> Senior Research Scientist
> Stanford Center for Narcolepsy Research
> 701-B Welch Road, Room 119
> Palo Alto, CA 94304  U.S.A.
> tel:  1-650-724-4087   fax: 1-650-725-4913
> http://www.med.stanford.edu/school/Psychiatry/narcolepsy/
>
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