Question: How to find the self aligned repeat region in human genome
0
gravatar for Chen
4.1 years ago by
Chen910
Chen910 wrote:

Is there a database for the self aligned repeat region. What I mean is to mark the region that are duplicated inside the chromosome or genome itself. Usually these regions are hard to find exact read mapping, because reads from these region can be mapped to multi repeat locations.

I look at repeatmasker's database(http://www.repeatmasker.org/species/hg.html), they only report 1. low complexity region, 2. region similar with reported repeat sequences such as Alu.

ADD COMMENTlink modified 4.1 years ago by Pierre Lindenbaum123k • written 4.1 years ago by Chen910
3
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

see http://hgdownload.cse.ucsc.edu/goldenPath/hg38/vsSelf/

 

This directory contains alignments of Human (hg38, Dec. 2013, GRC Build GRCh38) to itself,
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Pierre Lindenbaum123k

Thanks, that really helps

ADD REPLYlink written 4.1 years ago by Chen910

Actually, the result of UCSC is not 100% report, I find lots of false negatives. And the tools they are using is blastz from Penn State University.

ADD REPLYlink written 4.1 years ago by Chen910

Is there any similar data set for Bos taurus (UMD3.1)?. I've browsed UCSC and Ensembl corresponding directories.

ADD REPLYlink written 2.2 years ago by serpalma.v20
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