[Genome] What up with the #bin?

[Hiram Clawson]

Good Morning Dr. Becker:

This is a scheme to speed up MySQL queries.  Items are assigned
to a bin based on their chromosome coordinate.

As described in this paper:
http://www.genome.org/cgi/content/abstract/12/6/996
Genome Res. 2002 Jun;12(6):996-1006.
The human genome browser at UCSC.
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D.

Please note Figure 7 in that paper.  The scheme has been
expanded since then to include one more top-level bin size of 4Gb.
There is an exerciser and test program in the kent source
tree src/hg/lib/tests/binTest.c

--Hiram

Becker, Kevin (NIH/NIA/IRP) [E] wrote:
> Hello genome folks,
> 
>  
> 
> In the UCSC table downloads, such as mgcGenes, the first column is #bin.
> 
> What's that?
> 
>  
> 
> Presumably genes are binned into groups, but how?
> 
>  
> 
> Sincerely,
> 
>  
> 
> KGB
> 
>  
> 
> Kevin G. Becker Ph.D. 
> Head, Gene Expression and Genomics Unit 
> Deputy Chief, Research Resources Branch 
> NIH Biomedical Research Center
> 
> 251 Bayview Boulevard, Room 4B211
> National Institute on Aging 
> National Institutes of Health 
> Baltimore, MD 21224 
> TEL:   410-558-8360 
> FAX:  410-558-8236 
> beckerk at grc.nia.nih.gov <mailto:beckerk at grc.nia.nih.gov>  
> http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm
> <http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm>