Is there some good software to automatically annotate a DNA sequence? I'm dealing with a specific situation right now, but it would be nice to have a general tool that just takes a DNA sequence and automatically annotates it well based on information from databases. In my situation right now, I am looking at chimeric transcripts in cancer cells where two transcripts from different genes are fused together. Therefore, I get a sequence, blast it, find out which part matches with transcript A, find out which part matches with transcript B, and then I annotate it using APE (Advanced Plasmid Editor) to mark which part of the sequence corresponds to transcript A and B, the start codon, the stop codon. I can then acquire some useful information such as the protein produced, and the protein sequence after the fusion point. Anyway, does anyone have a good recommendation for automatically annotating DNA sequences?
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