Is there a way to fetch genomic sequences at given coordinates without downloading fasta files?

Question: Is there a way to fetch genomic sequences at given coordinates without downloading fasta files?

2.2 years ago by

So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the genome as a fasta file and then use pyfaidx to extract the sequences at the given positions. But now that I'm working with several species at once, I was wondering if there's any kind of tool in Python or R that can fetch your sequences of interest without downloading a bunch of large files. Thanks

dna R sequence python genome • 1.7k views

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modified 2.2 years ago by Matt Shirley ♦ 9.2k • written 2.2 years ago by ericbrenner • 0

Please do not cross-post to BioStars and Stack Exchange https://bioinformatics.stackexchange.com/questions/2543/way-to-get-genomic-sequences-at-given-coordinates-without-downloading-fasta-file

ADD REPLY • link written 2.2 years ago by Emily_Ensembl ♦ 20k

2.2 years ago by

Satyajeet Khare • 1.5k

Pune, India

Satyajeet Khare • 1.5k wrote:

Here is one way to download the sequences using DAS server. You can write a loop and fetch the sequences.

ADD COMMENT • link modified 2.2 years ago • written 2.2 years ago by Satyajeet Khare • 1.5k

2.2 years ago by

Emily_Ensembl ♦ 20k

EMBL-EBI

Emily_Ensembl ♦ 20k wrote:

You can use the Ensembl REST API.

ADD COMMENT • link written 2.2 years ago by Emily_Ensembl ♦ 20k

Does "GET sequence" on the REST API work for previous assemblies/releases of other species? I only know how to do it for grch37, but is that it. Thanks :)

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by ericbrenner • 0

Unfortunately not. We've recently started making REST access archives, which can get you to previous assemblies, but only recent archives are available and the only assembly that's changed in that time is pig. So actually, the answer is yes for pig and for human GRCh37 (as you've discovered), no for any other species.

ADD REPLY • link written 2.2 years ago by Emily_Ensembl ♦ 20k

2.2 years ago by

Matt Shirley ♦ 9.2k

Cambridge, MA

Matt Shirley ♦ 9.2k wrote:

There's a project called genomepy that handles the genome downloads and uses pyfaidx as the interface for queries. You could give that a shot, but you'd still be downloading files, just abstracting away the downloading process.

ADD COMMENT • link written 2.2 years ago by Matt Shirley ♦ 9.2k

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