Which Genomic Coordinates Does Cen Map To?

Question

[Jimineep]

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!

[Obi Griffith]

Even though the answers to these questions might be subtly different, I feel like they really belong in the same question.

Answer 1

[Dm Church]

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?

[Jimineep]

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!

[Dm Church]

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.

[Jimineep]

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.