I am using Augustus to predict genes. It works well most of the time. However I am dealing with a problem of translation of the extracted codingsequences. I use getAnnoFasta.pl to extract the codingseq and the aminoacids also. If I am not wrong, the codingSeqs should translate exactly the aminoacids sequences. This is not the case in several instances. When I checked my coding seq and translate them many results in other protein totally different form the file containing the aa sequences. Is this a common problem?. Is this best way to extract sequences?. I tried to use the GFF and loaded in artemis to edit error and I noticed that some features lost the frame. Maybe I am missing something.
Thanks
Thanks
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