[Genome] txCdsPredict score

[Polgera]

Hi,



Can you please give me more information about the txCdsPredict score? How
exactly was it obtained? What is the txCdsPredict program? Can I access the
program and generate the score myself? How reliable is it and how does it
compare to other programs like CRITICA? Is there another name for it? I
can't seem to find evidence of this score being used in the literature.
Also, what are the maximum and minimum scores? How would I interpret it if
it is say 400 instead of 800? And what does it mean if the score is negative
versus positive?



Thank you sincerely.

[Jennifer Jackson]

Hello Polegra,

This program is used as part of the UCSC Genes track building process.
Basically, the program is used to call the open reading frame for
transcripts in the track (except for RefSeq and CCDS derived).

A reference to the program is in the Methods, step 8, on the UCSC Genes
track description page (open browser to an assembly with a UCSC Genes
track, ex: hg19, and click on the track name to view the description
with Methods, Credits, References, etc.).

The program is in the kent source tree here:
kent/src/hg/txCds

description of kent source utilities:
http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities

source download (build instructions in source tree):
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27

ftp download of pre-compiled versions of selected programs (this program
is not included):
http://hgdownload.cse.ucsc.edu/admin/exe/

It may be possible to provide you with additional documentation. We will
send an update.

Thank you for your patience while we gathered the details for your answer,
Jennifer

---------------------------------
Jennifer Jackson
UCSC Genome Informatics Group
http://genome.ucsc.edu/

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