question

[reihaneh fazeli]

Dear Sir/Ms.
We designed a linkage analysis for a gene involved in autosomal
recessive nonsyndromic hearing loss (STRC) in the Iranian population. One of our major concerns is to find good STR markers. Would you please tell me how I can find STR markers using the UCSC genome browser? I would be more than thankful if you introduce me a good material (a book or preferentially a CD)
to learn how to work with the UCSC genome browser. I am eagerly looking forward to hearing from you.

Thank you in advance.


Reihane fazeli
Department Of molecular biology

pathobiology laboratory center

Gharani Alley

Valiasr St

After Chamran Intersection                                                     

Tehran
Iran
Tel:+98-21-22666563

[Brian Lee]

Dear Reihane,

Thank you for using the UCSC Genome Browser and your question about how to find  short tandem repeats (STR) markers using the UCSC genome browser.

In the UCSC Genome Browser we do have a way to visualize STRs in a Simple Tandem Repeats by TRF track, however, it does not include allele or frequency count information, which you are likely interested in as you investigate the polymorphism among individuals in the STRC gene you have found related to the hearing loss you are studying.

The reason this track does not have variant information is that the track on the UCSC Genome Browser represents the results of programmatic annotations via a Tandem Repeats Finder (TRF) program. I recommend reviewing this previously answered mailing-list question, https://groups.google.com/a/soe.ucsc.edu/g/genome/c/aQnrmQFQmZ0/m/KSUj2inICQAJ, where to help demonstrate the programmatically generated track there is a session that includes a Short Match track.  The session is highlighting the sequence ctctcgct within the window and this reflects how a programmatic approach can annotate the genome, where TRF helps discover and annotate possibly imperfect repeats as well as exact matches: http://genome.ucsc.edu/s/brianlee/hg38_STR This session can even be redirected to the STRC gene with this following link: http://genome.ucsc.edu/s/brianlee/hg38_STR?singleSearch=knownCanonical&position=STRC&knownGene=pack

In that previous mailing-list question where a user similar to you was looking for  STRs with allele or frequency count information, we suggested looking into the resources at STRBase https://strbase.nist.gov/index.htm which was founded in 2001 and includes a Variant Allele Reports page for STRs.

In case you are interested in still learning more about the Browser, we do have a training page, and on that page there is a link to our YouTube channel, where transcripts of the discussed topics are also available for review: http://genome.ucsc.edu/training/index.html#videos

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.

All the best,

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