This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting Nucleotide Based From Ucsc Or Ensembl?

Possible Duplicate:
How to get the sequence of a genomic region from UCSC?

Hi all, I wanted to know if there was a way to query UCSC or Ensembl to get the nucleotide at a specific chromosomal location such as 

Chromosome 11: 123524481

Thanks in advance.

Ashwin

ucsc ensembl sequence retrieval
• 3,373 views • link
updated by Sean Davis Sean Davis • written by Ashwin • Ashwin

I see this is closed, but I can't find the duplicate question. You can do this with the Ensembl Perl API: define a 'slice' of one nucleotide, and get the sequence- see this tutorial:

http://www.ensembl.org/info/docs/api/core/core_tutorial.html#slices

Alternatively, 'Export Data' from the Location Tab of the Ensembl browser. You can change your location and export the sequence in the window once you click 'Export Data':

http://www.ensembl.org/Homo_sapiens/Location/View?r=6:133017695-133161157

Of course the Perl API will be the better solution is you have many locations!

• 0 views • link
updated by Ram Ram • written by Giulietta - Ensembl Helpdesk Giulietta - Ensembl Helpdesk

1 answer

You can use the UCSC DAS server like so (for hg19, as an example):

curl "http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr11:123524481,123524481"

Which will return:


http://www.biodas.org/dtd/dasdna.dtd">
<DASDNA>
<SEQUENCE id="chr11" start="123524481" stop="123524481" version="1.00">
<DNA length="1">
a
</DNA>
</SEQUENCE>
</DASDNA>

See the UCSC DAS server FAQ for details.

If you have many of these queries, you are better off downloading the fasta sequence and using libraries for R, python, perl, or java that can randomly query fasta files.

• 0 views • link
updated by Ram Ram • written by Sean Davis Sean Davis

Log in to answer this question.

More posts like this
  • How To Extract Rrna Sequences (In Fasta Format) From Genbank (Bacterial Genome)?
    written by microbeatic microbeatic
    <p>In the genbank files rRNA only have following features to it:</p> <blockquote> <pre><code> rRNA 67149..68657 /locus_tag="Arad_5100" /product="16S ribosomal RNA (operon 1)" /db_xref="GeneID:7371836" </code></pre> </blockquote> <p>unlike …
  • Domain Prediction In Globplot
    written by User 3325 User 3325
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/14516/domain-prediction-tool">domain prediction tool </a> </p> </blockquote> <p>is GLobPlot works for novel protein? can it predict domain of novel protein?</p>
  • 'What Scholarships Are Available In The Uk'.
    written by Ammu • Ammu
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/11734/please-help-me">Please help me…</a> </p> </blockquote> <p>Please inform, if there are any scholarships for Msc(bioinformatics) in Uk.</p>
  • Can Bam File Be Converted To Fasta Format?
    written by Hmm • Hmm
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file">Convert bam file to fasta file</a> </p> </blockquote> <p>Can we convert a whole human genome bam file into fasta format. …
  • Can The Coding Region Of One Gene Be The Non-Coding Region Of Another Gene?
    written by Saher Faiza • Saher Faiza
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/8771/gene-coding-and-non-coding-regions">Gene coding and non-coding regions</a> </p> </blockquote> <p>can a coding region of one gene be the non-coding region in another …
  • How Can I Retrieve All Of Human Promoter Sequences?
    written by Mohammad Reza Bakhtiarizadeh Mohammad Reza Bakhtiarizadeh
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/888/how-to-get-promoter-sequences-for-human-genes">How to get promoter sequences for human genes?</a> </p> </blockquote> <p>Hi all, I need all of human promoter sequences and …
  • How To Calculate The Protein Change And Codon Position Within A Nucleotide Sequence Of A Single Nuc…
    written by Blunders • Blunders
    <p>Appears that there is a misunderstanding on my part, and this question is an attempt to sort out these conflicts.</p> <p><strong>Definitions:</strong></p> <ul> <li><strong>Protein change</strong> being …
  • Forward In The Final Report
    written by Maria Angelica • Maria Angelica
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/4893/illuminas-genome-studio-final-report-forward-or-top-allele">Illumina’s Genome Studio Final Report: forward or top allele?</a> </p> </blockquote> <p>Allele - forward in the final report corresponds to …
  • Difference Between Coverage And Read Depth ?
    written by Monzoor • Monzoor
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/638/what-is-the-sequencing-depth">What is the sequencing ‘depth’ ?</a> </p> </blockquote> <p>What is the difference between coverage and read depth ?</p>
  • Extract A Sequence From Ucsc
    written by Litali • Litali
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/56/how-to-get-the-sequence-of-a-genomic-region-from-ucsc">How to get the sequence of a genomic region from UCSC?</a> </p> </blockquote> <p>Hello, I want to receive the sequence …