I am not quite understanding the output of the .predict file from Glimmer3.02 ORF predictor.
Here's a sample of the output file
ref|NC_023013.1| Haloarcula hispanica N601 chromosome 1, complete sequence orf00001 1 1575 +1 18.88 orf00003 2355 1645 -1 12.87
According to the documentation, column1= ID, column2=start of gene, column3= stop of gene, column4=reading frame, column5=The per-base “raw” score of the gene.
My questions are:
- to calculate the ORF score (100*log-odd ratio) of the gene, do I multiply column5 by the length of the gene?
- Is there a good threshold (either for column 5 or the calculated score) to see if the predicted ORF is likely to be true?
Thanks for the help!