Hello Nacho,
Please see these previously answered mailing list questions for discussion on exon frames: http://www.soe.ucsc.edu/pipermail/genome/2006-December/012425.html http://www.soe.ucsc.edu/pipermail/genome/2006-November/012218.html 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 Nacho Molina Clemente (Group Nimwegen) wrote: > Dear Mr/Ms/Miss, > > I am a postdoc in van Nimwegen's group from the Biozentrum (Basel). I > am using the human gene annotations that are provided by the UCSC web > site. In particularly, I am using the file refGene.txt that can be > downloaded here: > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ > > I am a bit confused regarding how to interpret the frames of the > exons. I have checked several cases (exons in the positive strand) in > the UCSC genome browser and, surprisingly, I found that if the frame of > the exon is 0 then the codon starts in the second base. If the frame is > 1 then the codon starts in the first base. And finally, if the frame is > 2 then, as expected, the codon starts in the third base. Is this normal? > Am I doing something wrong? Any indication of how to interpret the > frames or where to find a detailed description of the file refGene.txt > would be very helpful. Thank you very much in advance for your time and > your help. > > Best regards, > Nacho Molina. > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
