[Genome] target scan results..

[Juliette Faraco]

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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