Question: Translating a noval DNA sequence to protein
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gravatar for Jessica
11 weeks ago by
Jessica0
Jessica0 wrote:

If I have genomic DNA sequence of an organism, what are the tools I can use to predict the proteins encoded by it?

dna protein translate • 193 views
ADD COMMENTlink modified 11 weeks ago by Elisabeth Gasteiger1.9k • written 11 weeks ago by Jessica0
1
gravatar for Mensur Dlakic
11 weeks ago by
Mensur Dlakic8.1k
USA
Mensur Dlakic8.1k wrote:

In general, the first task would be to predict genes, from which proteins are predicted in straightforward fashion by translation. I will give you couple of links that may be useful:

Predicting genes in prokaryotes is relatively straightforward and is usually done with high accuracy. This is because prokaryotic genomes have something called high gene density (most of their DNA is coding for genes) and their genes are continuous (in one piece). I suggest you try prodigal for prokaryotice gene prediction.

Eukaryotic genes are more difficult to predict, and that first link is mostly about eukaryotic gene prediction. This is because they have lower coding density and genes are discontinuous (there are introns that have to be cut out and exons to be spliced together). There are many programs for this purpose, and they are in general less successful in accurately predicting gene locations and structure.

ADD COMMENTlink written 11 weeks ago by Mensur Dlakic8.1k
0
gravatar for Elisabeth Gasteiger
11 weeks ago by
Geneva
Elisabeth Gasteiger1.9k wrote:

For a very basic nucleotide to protein sequence translation tool you could try the Expasy Translate tool: https://web.expasy.org/translate/

ADD COMMENTlink written 11 weeks ago by Elisabeth Gasteiger1.9k
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