[Genome] Hello UCSC Genome browser staff

[Kayla Smith]

Hello Erez,

Tables can be downloaded here: 
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/

Some tables you may be interested in are:

   knownGene -this has ucsc gene names and coordinates, or refGene -this 
has refSeq accession names and coordinates.  Both have exon counts.

   rmsk or simpleRepeat -have repeat information (the rmsk table is per 
chromosome)

   cpgIslandExt -has CpG island data

   cytoBandIdeo -describes the positions of cytogenetic bands with a 
chromosome

Go annotations are found in a separate database, the tables for which 
can be downloaded from here:
http://hgdownload.cse.ucsc.edu/goldenPath/go/database/

Similar tables can be found in the mouse mm8 downloads section.  I hope 
this information is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


> Hello UCSC Genome browser staff,
> 
> I am seeking for specific tables in the annotation database (Human & Mouse)
> and am a bit overwhelmed by the size of your database..
> 
> Would you be so kind to tell me which tables do I need in order to get (by
> genomic coordinates):
> - The nearest gene (accession, name,..)
> - The nearest repeat
> - The nearest CpG islands
> - chromosome stain-band
> - (if inside a gene) The exon number, The GO annotations
> 
> Also, are these tables given per-chromosome or for the entire genome?
> 
> Thank you in advance,
> Erez Livneh
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
> From - Mon