[Genome] Find Genbank accession numbers based on positions

[Jason Ting]

Ann,

Thanks for the info. I checked out the suggested tables and found that they are not what I'm looking for.

What I need to do is, giving a list of positions, something like:

chr1  12345060  13456080
chr5  93403220  98340304
chrX  113043423  115234202

I need to find out all the GeneBank Accession Numbers located within each of those regions by using the Table Browser.

The difficaulty I'm finding is that while I can get the gene names, etc., I can't figure out how to get the GB Access Numbers out of the table browser.

Could you advise which table, or tables combined, will provide me the GB ANs?

Thanks in advance!

Jason



>>> Ann Zweig <ann at soe.ucsc.edu> 04/18/08 5:41 PM >>>
Hello Jason,

	The Table Browser feature you will need to use is the 'defined regions' 
button.  This will allow you to restrict your table search to the 
positions you enter, like so:

chrX   151073054   151173000
chrX   151183000   151190000
chrX   151283000   151290000

	You will have to decide which table you would like to search based on 
exactly which Genbank items you would like.  For example, we have an 
mRNA annotation track in the browser that displays alignments between 
human mRNAs in GenBank and the genome.  The underlying table is named 
"all_mrna".  Configure the table browser like so to query that table for 
the positions you are interested it:

group: mRNA and EST Tracks
track: Human mRNAs
table: all_mrna

	Alternatively, you could use data from the Human EST track.  The 
underlying table for this track is called "all_est".  If you are 
interested in RefSeq Genes, use that track (the table is "refGene").

	This should be enough to get you started.  If you need more detailed 
information, please don't hesitate to write back to the list.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Jason Ting wrote:
> Dear UCSC,
> 
> I would like to locate Genebaml accession numbers in table browser by using info of chromosome:positions.
> 
> Please advise which table or tables I should I be using.
> 
> Thanks,
> 
> Jason Ting
> 
> 
> 
> 
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