get genomic location
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mali salmon ▴ 350
@mali-salmon-4532
Last seen 3.0 years ago
Israel
Hello List I have a basic question. Is there an easy way to convert a location in protein and mRNA to genomic location? (except of alignment...) For example, I have a list of point mutations in amino acids positions and/or positions in mRNA, and I would like to get their genomic locations. Thanks Mali [[alternative HTML version deleted]]
Alignment convert Alignment convert • 1.3k views
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@valerie-obenchain-4275
Last seen 23 months ago
United States
Hi Mali, Unfortunately we don't have a function that converts from protein- based to genomic-based coordinates - at least I'm unaware of one. The conversion functions we do have are transcriptLocsToRefLocs() in GenomicFeatures and refLocsToLocalLocs() in VariantAnnotation. The first converts from transcript-based to genome-based and the second from genome-based to transcript and protein-based. Michael and I have plans to consolidate these coordinate-mapping functions into the single 'Map' generic in IRanges. This will likely be done for the next BioC release. Valerie On 06/12/2012 02:29 AM, mali salmon wrote: > Hello List > I have a basic question. > Is there an easy way to convert a location in protein and mRNA to genomic > location? (except of alignment...) > For example, I have a list of point mutations in amino acids positions > and/or positions in mRNA, and I would like to get their genomic locations. > Thanks > Mali > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Wed, Jun 13, 2012 at 6:46 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote: > Hi Mali, > > Unfortunately we don't have a function that converts from protein- based > to genomic-based coordinates - at least I'm unaware of one. The > conversion functions we do have are transcriptLocsToRefLocs() in > GenomicFeatures and refLocsToLocalLocs() in VariantAnnotation. The first > converts from transcript-based to genome-based and the second from > genome-based to transcript and protein-based. > > Although transcriptLocsToRefLocs would come really close. We would just have to adjust for the translation start. > Michael and I have plans to consolidate these coordinate-mapping > functions into the single 'Map' generic in IRanges. This will likely be > done for the next BioC release. > > Valerie > > > > On 06/12/2012 02:29 AM, mali salmon wrote: > > Hello List > > I have a basic question. > > Is there an easy way to convert a location in protein and mRNA to genomic > > location? (except of alignment...) > > For example, I have a list of point mutations in amino acids positions > > and/or positions in mRNA, and I would like to get their genomic > locations. > > Thanks > > Mali > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]
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