Hello Ivan,
Details about how this track in incorporated into the UCSC database is
documented in the source tree.
http://genome-test.cse.ucsc.edu/~kent/src/unzipped/hg/makeDb/doc/ccds.txt
excerpt:
# ccdsKgMap
/cluster/data/genbank/bin/x86_64/mkCcdsGeneMap -db=${db} -loadDb
ccdsGene knownGene ccdsKgMap
The program mkCcdsGeneMap is also in the source code. It is run with the
default 0.95 (95% similarity) of the CDS regions of UCSC Genes vs CCDS.
Specifically, similarity is calculated by
min(numberOfBasesInCommon/sizeof(ccds),
numberOfBasesInCommon/sizeof(ucscGeneCDS))
mkCcdsGeneMap - create with mappings between ccds and other gene tables
Usage:
mkCcdsGeneMap [options] ccdsTblFile geneTblFile ccdsGeneMapOut
Create a mapping between CCDS and other gene tables based on similarity
of the genomic location of the CDS. The ccdsTblFile, and geneTblFile
arguments are genePreds and can be tables or files. The ccdsGeneMapOut
specifes the table and tab file to create to load the database, it's
base name is also the table name. If a simple table name is supplied, a
.tab extenions is added. The table is first loaded with an _tmp
extension and then renamed if the load succeeds.
Options:
-db=db - database if tables are being read or loaded
-similarity=0.95 - require at least this level of similar
-loadDb - load table into db
-noopNoCcdsTbl - if specified, it's the program will exit without
error if there is no CCDS table. Requires -db.
-keep - keep tmp tab file used to load database
-verbose=n
We hope this helps. Please feel free to contact the mailing list support
team again if you would like more assistance.
Warm regards,
Jen
UCSC Genome Browser Support
mkCcdsGeneMap is run with the default 0.95 (95% similarity) of the CDS
regions
of knowngenes vs ccds. Similarity is calculated by
min(numberOfBasesInCommon/sizeof(ccds),
numberOfBasesInCommon/sizeof(ucscGeneCDS))
Please feel free to contact the mailing list support team again if you
would like more assistance.
Warm regards,
Jen
UCSC Genome Browser Support
On 7/31/10 8:22 PM, Ivan Adzhubey wrote:
> Hi,
>
>> From ccdsKgMap table description:
>
> Schema for ccdsKgMap
> Database: hg19 Primary Table: ccdsKgMap Row Count: 38,095
> Format description: mapping between CCDS ids and Known Genes by similarity
>
> cdsSimilarity 1 float range CDS similarity by genomic
> overlap
>
> Similarity to what? To the genomic reference sequence? How it is calculated? A
> formula would be nice.
>
> Thanks,
> Ivan
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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