[Genome] Human/Chimp Annotation Files

[Archana Thakkapallayil]

Hello James,

You could get this information using any of the gene prediction tracks 
in either assembly, such as Known genes, RefSeq genes, N-SCAN , Genscan 
genes etc. You can either use the Table Browser to get the selected 
fields from the respective tables or download the tables in bulk from 
our download server at:

http://hgdownload.cse.ucsc.edu/downloads.html

 From here choose the organism you are interested in and then choose 
'Annotation database'.

The corresponding files are:
knownGene.txt.gz
refGene.txt.gz
nscanGene.txt.gz
genscan.txt.gz

More information on using the Table Browser is here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

I hope this information is helpful to you. If you have further 
questions, please do not hesitate to contact us again.

Regards,

Archana
UCSC Genome Bioinformatics Group


James C Farslow wrote:
> Hello,
> We are trying to identify duplicated ORFs in the human ad chimp 
> genomes.  I tried to find annotation files on your website, but have 
> not had any luck looking for what we need.  Do you have any files that 
> provide:
>
> An ORF name;
> the chromosome;
> the ORF start and stop positions;
> the strand (+/- or W/C).
>
> We are specifically looking for known or predicted ORFs, not transcript 
> or microarray data.  Positions of known exons/introns would be useful, 
> but not required.
>
> Your time and assistance in this matter would be greatly appreciated.
>
> Thank you.
>
> James Farslow
> jfars at unm.edu
> Bergthorsson Lab
> University of New Mexico, Biology Dept.
>
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