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Blast2GO is pretty good for that, I don't think it will identify fusion transcripts though. -
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?
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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