[Genome] GenePred Format

[Alden Huang]

Hi,

I just had a quick question...

In the description of the Gene Predictions table format used by UCSC,
under specifically Gene Predictions (Extended), it lists two fields:

string cdsStartStat; "enum('none','unk','incmpl','cmpl')"
string cdsEndStat; "enum('none','unk','incmpl','cmpl')"

I would simply like to know the significance of these particular fields.

thanks,

alden

[Katrina Learned]

Hi Alden,

These fields provide additional information about the status of the
start and end of a gene's coding region. The possible statuses are:

- none - no CDS specified from the sequence's data source.
- unk - unknown - not known if CDS start/end is complete.
- incmpl - the CDS start/end is incomplete
- cmpl - the CDS start/end is complete.

cdsStartStat refers to the cdsStart end of the gene, which is the start
codon for a positive strand gene and the stop codon for a negative
strand gene. cdsEndStat refers to the cdsEnd end of the gene, which is
the stop codon for a positive strand gene and the start codon for a
negative strand gene.

Please don't hesitate to contact the mail list again if you have any
further questions.

Katrina Learned
UCSC Genome Bioinformatics Group

Alden Huang wrote, On 02/18/11 16:32:

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