[Genome] RefSeq xeno, species filtering

[Kayla Smith]

Hello John,

The key relationship here is that gbCdnaInfo.organism = organism.id

In particular,

mysql> select * from organism where name like "homo sapiens" ;
+-----+--------------+-----------+
| id  | name         | crc       |
+-----+--------------+-----------+
| 298 | Homo sapiens | 455363425 |
+-----+--------------+-----------+
1 row in set (0.00 sec)

and

mysql> select acc, organism from gbCdnaInfo where organism=298 limit 1;
+--------+----------+
| acc    | organism |
+--------+----------+
| U61167 |      298 |
+--------+----------+
1 row in set (0.00 sec)

You can check that this accession is from Human.

So, how to get this information from the Table Browser is as follows:

clade: Vertebrate
genome: Rhesus
assembly: Jan. 2006
group:  Genes and Gene Prediction Tracks
track: Other RefSeq
table: xenoRefGene
region: genome
filter: "create"
   -under "Linked Tables" check the box next to rheMac2.gbCdnaInfo and 
then click on "Allow Filtering Using Fields in Checked Tables"
   -toggle "organism" is = "298"
   -click "Submit"

This should filter the results to get you the data you're interested in.

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



Castle, John (Rosetta) wrote:
> Hi UCSC,
> 
> Great resource.
> 
> I'm looking at the rhesus genome and specifically at the other species
> RefSeq transcript alignments.  I can use the table browser to extract
> coordinates - no problem.  However, I would like to filter the list of
> xeno RefSeqs to include only human RefSeqs.  I've tried the 'filter'
> option but haven't been able to find where/how the species designations
> for the xeno RefSeqs is found/designated.
> 
> Thanks for any guidance!
> 
> -John
> 
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