A Way To Get Dna Sequence From Specific Coordinates Using An Online Service

Question

[KCC]

Is there an easy way, using some online service, to retrieve a bit of sequence from the C. elegans genome. As an example, I could enter chromsome 4 and position 5,000,000 to 5,002,000 and get the DNA sequence in that location.

I know how to do this from the command line, but I'd like a much easier way for people who don't use the command line.

Answer 1

[Hamish]

Well the first way that comes to mind is using Ensembl or Ensembl Genomes:

1. Go to the C. elegans Ensembl: http://www.ensembl.org/Caenorhabditis_elegans/, or the C. elegans Ensembl Genomes: http://metazoa.ensembl.org/Caenorhabditis_elegans/, these are using the same genome build so the choice is up to you.
2. Search for the required genome region by typing it into the search box, in your case the region is "IV:5000000-5002000", and click the "Go" button
3. Click the "Export data" item in the left-hand menu
4. Select the required format, etc. and click "Next"
5. Select how you want to view/download the sequence data for the region.

You could of course also do this by constructing the URL used to access the result, for example:

http://www.ensembl.org/Caenorhabditis_elegans/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=IV:5000000-5002000;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text

or:

http://metazoa.ensembl.org/Caenorhabditis_elegans/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=IV:5000000-5002000;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text

But that is only really worth it if you are going to fetch a lot of sections from these genomes.

I suspect that the same thing can be achieved using WormBase but I haven't used it much so I'm not sure how to go about it there.

Answer 2

[Emily]

A really easy way to get this data would be using the Ensembl REST API sequence_region module. Details are here:

http://beta.rest.ensembl.org/documentation/info/sequence_region

In essence you can make a URL like this:

http://beta.rest.ensembl.org/sequence/region/caenorhabditis_elegans/IV:5000000..5002000:1?content-type=text/plain

Which will just take you to a page with the sequence.

Change the species and coordinates to suit your purpose.

Answer 3

[Pierre Lindenbaum]

same as

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

use the DAS server of the UCSC:

http://genome.ucsc.edu/cgi-bin/das/ce6/dna?segment=chrII:1,100000