program to automatically annotate a DNA sequence

azim58 · 06-27-2014, 04:06 PM

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?

Jeremy · 07-01-2014, 01:23 AM

Blast2GO is pretty good for that, I don't think it will identify fusion transcripts though.

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06-27-2014, 04:06 PM	#1
azim58 Junior Member Location: Tempe AZ Join Date: Jun 2014 Posts: 6	program to automatically annotate a DNA sequence 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?

07-01-2014, 01:23 AM	#2
Jeremy Senior Member Location: Pathum Thani, Thailand Join Date: Nov 2009 Posts: 190	Blast2GO is pretty good for that, I don't think it will identify fusion transcripts though.