STR information
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Florian
Jan 7, 2021, 12:30:35 PM1/7/21
to gen...@soe.ucsc.edu
Dear Sir or Madam,
I am looking for specific Short Tandem Repeat sites in the GRCh38
genome. I found that I could extract information using the Table Browser
but, while it shows the mean number of unit for each STR, I would need
the identity of each existing allele and their count (or frequency). Is
there a database that I missed where I could find this information ?
Thank you very much in advance.
Best regards,
--
Florian Mauffrey
I am looking for specific Short Tandem Repeat sites in the GRCh38
genome. I found that I could extract information using the Table Browser
but, while it shows the mean number of unit for each STR, I would need
the identity of each existing allele and their count (or frequency). Is
there a database that I missed where I could find this information ?
Thank you very much in advance.
Best regards,
--
Florian Mauffrey
Brian Lee
Jan 8, 2021, 5:18:26 PM1/8/21
to Florian, UCSC Genome Browser Mailing List
Dear Florian,
Thank you for using the UCSC Genome Browser and your question about Short Tandem Repeats (STRs) information.
Our Simple Tandem Repeats by TRF track does not include allele or frequency count information. The reason for this is that the track represents the results of programmatic annotations via the Tandem Repeats Finder (TRF) program. You can read more about the data behind the track on the track description page which references this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148217/
To help demonstrate the track here is a session that includes a Short Match track that is simply 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
You may be interested in a resource called STRBase https://strbase.nist.gov/index.htm which was founded in 2001 but remains updated as recently as just last month and includes a Variant Allele Reports page for STRs.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Thank you for using the UCSC Genome Browser and your question about Short Tandem Repeats (STRs) information.
Our Simple Tandem Repeats by TRF track does not include allele or frequency count information. The reason for this is that the track represents the results of programmatic annotations via the Tandem Repeats Finder (TRF) program. You can read more about the data behind the track on the track description page which references this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148217/
To help demonstrate the track here is a session that includes a Short Match track that is simply 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
You may be interested in a resource called STRBase https://strbase.nist.gov/index.htm which was founded in 2001 but remains updated as recently as just last month and includes a Variant Allele Reports page for STRs.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
--
---
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Brian Lee, QA Manager
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