Webservice For Translation Of Genomic Positions Between Builds?

Is there a web service for translating a genomic position from one reference build to another?

For instance:

I have an arbitrary position chr1:1234567 in hg18 and I want to know what the equivalent position is in hg19 (GRCh37).

I want to do this without running my own alignment in order to save time/complexity so I figured maybe there was somebody out there running a service that could handle this.

alignment software mapping genome

• 3,171 views • link

updated 5.3 years ago by Ram

• written 15.5 years ago by Ryan W.

2 answers

It's not a so-called 'web-service' but did you try liftOver?

• 1 views • link

updated 6.9 years ago by Ram

• written 15.5 years ago by Pierre Lindenbaum

This is interesting, and it's supplied directly by UCSC. It's not immediately apparent how to incorporate this into my app so I'll have to experiment with it more. Thanks for the link, though.

• 0 views • link

updated 5.4 years ago by Ram

• written 15.5 years ago by Ryan W.

Two web sources I know of:

Galaxy has liftOver
Ensembl has Assembly converter

EDIT:

The ensembl url also has a link to the perl API, which could be integrated into soaplab if you wanted a web 'service' rather than a web site.

• 2 views • link

updated 5.3 years ago by Ram

• written 15.5 years ago by Alastair Kerr

I think that ensembl API is going to be what I need. Thanks for the answer.

• 0 views • link

updated 5.3 years ago by Ram

• written 15.5 years ago by Ryan W.

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