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/ On 3/30/10 11:13 AM, Polgera wrote: > 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. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
