Hey.
Apologies for the similarity to the previous question I asked (http://biostar.stackexchange.com/questions/18969/which-genomic-coordinates-do-pter-and-qter-map-to) but I thought it might be better to have separate questions since the details might be a bit different
I've downloaded this file to map between cytoband locations and genomic coordinates:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
following suggestions here (thanks!)
http://biostar.stackexchange.com/questions/4363/how-to-obtain-chromosome-locus-from-coordinates
However I have locations such as:
6p21.1-cen
or
2cen-q13 (both taken from OMIM morbid map)
I am not sure what ranges these refer to. Any ideas?
Thanks a lot!
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written
by
Jimineep •
Typically cen stands for centromere. So 6p21.1-cen is band 6p21.1 to the centromere. The GRC (http://genomereference.org) attempts to model centromere lengths (using Ns that approximate the length of the centromere) in the assembly, so there should be a conversion for this- although I'm not entirely sure if 2cen is the proper nomenclature.
The definitive work on this is: http://content.karger.com/ProdukteDB/produkte.asp?Aktion=showproducts&searchWhat=books&ProduktNr=244102
Would a web page or service that takes a list of cytogenetic location and returns a list of sequence locations be useful?
Absolutely. I've written a tiny R function that does it when using the n[p,q]n.n nomenclature but it's pretty amateur, using the cytoband.txt file, and a helper function to retrieve the genes in that location via GenomicFeatures, but the cen and pter/qter things mess it up!
OK- we have the code to do this- we use it to support pages like this:http://www.ncbi.nlm.nih.gov/genome/tools/gdp
I'll see if we can get this set up as a public service/web site that folks can use.
Brilliant! I can imagine a lot of people need to do this regularly so if people hear about it I can imagine it getting a lot of use.
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Even though the answers to these questions might be subtly different, I feel like they really belong in the same question.