Convert p. Nomenclature to chromosomal coordinates

[Fisk, Dianna]

Hello,

 

I have rather long list of amino acid positions that are specified by p. nomenclature (e.g. NP_000129.3:p.Cys1032) that I need to convert into chromosomal coordinates (e.g. Chr15:48780677-48780679). I can do this one-at-a-time via the Genome Browser search box, which leads me to believe that I SHOULD be able to do a bulk query via the Table Browser, but I can’t quite figure it out. Is this possible? Do you have suggestions?

 

Thanks for your help!

 

Dianna Fisk, Ph.D. (she/her/hers)

Clinical Data (Genomics) Scientist

Clinical Genomics Progam · Stanford Health Care

3375 Hillview Ave · Palo Alto · CA 94304

df...@stanfordhealthcare.org C: 415-297-2358

 

[Matthew Speir]

Hello, Diana. 

Thank you for your question about converting amino acid positions to genomic coordinates in the UCSC Genome Browser. 

You can use the Variant Annotation Integrator (VAI) to convert positions on NM_* or NR_* accessions, but it does not support converting from NP_* accessions at this time. However, we are keen to implement this in the VAI and want your feedback on how the output should be formatted. Would you prefer:

a) a full back-translation that includes a list of possible nucleotide changes that would lead to the specified amino acid change (which could get long if there are multiple amino acids) in HGVS c. and/or g. notation

b) BED3 (chrom, start, end) of genomic position ranges corresponding to the changed amino acids

In the meantime, one of our engineers suggested the following tools that they have used for doing this conversion in the past:  

• Web tool: https://mutalyzer.nl/back-translator
• Or the underlying method as a python package: https://github.com/mutalyzer/crossmapper
• Other command-line + python package options:
• https://github.com/zwdzwd/transvar
• https://github.com/biocommons/hgvs
  

Note that we don't maintain any of the tools I've listed here, so questions regarding their use or bugs should be directed to their respective authors. 

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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