Question: Is there any way to find repetitive DNA in the promoter region for specific gene using bio conductor
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gravatar for M K
2.6 years ago by
M K460
United States
M K460 wrote:

I want to find what are the repeats in the promoter region for the following mouse genes Pole3,Prdx4,Stmn1. I used Bioconductor under R and I got all information and I got the promoter sequences (5kbp) for each of those genes using the following workflow in Bioconductor "Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching". Is there any other way to match repeats on found on those 5kbp promoter of genes

sequence next-gen R gene • 939 views
ADD COMMENTlink modified 2.6 years ago by Santosh Anand4.9k • written 2.6 years ago by M K460
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gravatar for Santosh Anand
2.6 years ago by
Santosh Anand4.9k
Santosh Anand4.9k wrote:

This is easy to do with UCSC Genome browser if you have only a few genes. After you get the chromosomal location of promoter region in UCSC format (chr:start-end), go to UCSC table browser https://genome.ucsc.edu/cgi-bin/hgTables

Choose group: 'variation and repeat' and track: 'repeatmasker '. Enter position (or if you have more than one, use the paste list radio button). Click 'get output' and you are done.

ADD COMMENTlink written 2.6 years ago by Santosh Anand4.9k
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