What Table Of Coordinates Is Used For "Minor" Bands In Paintcytobands From Quantsmooth From Bioconductor?

Question

[Pedrosaurio]

I am using the (great) paintCytobands function from quantsmooth to plot human chromosomal bands next to genomic data. As far as I understand, this function plots by default the 'major' bands using the coordinates from UCSC. If the bands parameter is set to anything different from "major" the ideogram will plot the 'minor' bands. Which bands are these and where can I find the table?

Answer 1

[Jan Oosting]

With data(chrom.bands) you will obtain a data.frame with all the information. Note that the table in the package is based on build 35.1 of the human genome. It can be found here ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/mapview/ideogram.gz

[Pedrosaurio]

Thank you very much Jan, actually I was expecting you to answer this question. I was already exploring the source code of paintCytobands and found the chrom.bands data frame. By any chance do you know any reference where they explain how these sub-bands were found or defined?

[Pedrosaurio]

I contacted people from NCBI about how they determined the coordinates of the sub-bands. They said that this data is unofficial and only for internal use. In addition this data will not longer appear in future updates of the ideogram files on the ftp site.

[Pedrosaurio]

The link above does not work any more. This is the new one

ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.35.1/mapview

[Pedrosaurio]

The link above does not work any more. This is the proper one:

ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.35.1/mapview/ideogram.gz

[Julien Textoris]

Dear Jan,

how can we load another organism cytoband dataset, for example mouse ? (but i don't know if it exists !!) ?

Thanks

Answer 2

[Pedrosaurio]

After one year I found the source:

A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome.

The sub-bands are just arbitrary segments, of the same length, of a each band, defined in order to create arbitrary references to increase precision of where do FISH probes map to the mitotic chromosomes.