Question: Getting Sequence Information From Ucsc Genome Browser
gravatar for anuragm
7.8 years ago by
anuragm130 wrote:

I had downloaded the Phast cons score for Xenopus tropicalis alignment with other vertebrate species to look for conserved regions. So, now I have the positions that I am interested in. How do I get the exact nucleotides corresponding to these positions now ?

nucleotide genome-browser • 2.6k views
ADD COMMENTlink modified 7.8 years ago by Alex Reynolds31k • written 7.8 years ago by anuragm130
gravatar for Alex Reynolds
7.8 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

A DAS query can help with automation.

For example, to write the human (hg19) sequence for a region on chromosome chrX at positions 1000000-1000010 to a file called foo.xml:

$ wget -O -,1000010 > foo.xml

The XML looks like this:">
<SEQUENCE id="chrX" start="1000000" stop="1000010" version="1.00">
<DNA length="11">

You can parse this on the command line, using an XSLT stylesheet and xsltproc.

First, create the stylesheet that retrieves the value of data in the sequence path; for example, foo.xsl:

<xsl:stylesheet xmlns:xsl="&lt;a href=" <a="" href="" rel="nofollow">" "="" rel="nofollow">' version='1.0'>
  <xsl:output method="text" encoding="UTF-8"/>
  <xsl:template match="/">
    <xsl:value-of select="DASDNA/SEQUENCE/DNA"/>

Then run the foo.xml result against this stylesheet:

$ xsltproc foo.xsl foo.xml | awk '($0 ~ /^[acgtnACGTN]/)'

You can glue some of this into a pipeline or shell script:

#!/bin/bash -efx


wget -O - ${DASURL}/${BUILD}/dna?segment=${CHR}:${START},${STOP} \
    | xsltproc foo.xsl - \
    | awk '($0 ~ /^[acgtnACGTN]/)' \
    > foo.txt
ADD COMMENTlink modified 7.8 years ago • written 7.8 years ago by Alex Reynolds31k
gravatar for Sean Davis
7.8 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

The high-level view may be enough to get you going.

  1. Convert your regions of interest into BED format
  2. Upload your BED file to the UCSC genome browser as a custom track
  3. Use the UCSC Table Browser, choose your custom track as the track of interest, then choose output "sequence"
ADD COMMENTlink written 7.8 years ago by Sean Davis26k
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