How To Identify The Secretion System In A Newly Sequenced Bacterial Genome?
I hava a newly sequenced genome containing several hundred of scaffolds.Now I want to know how many secretion systems there are in this strain.I have annotated the draft genome using RAST.But the annotation information can not tell whether a protein is involved in a scretion system.So how to find out what I want from the annotation results, or is there another way to get what I want? Thank you.
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Zev.Kronenberg
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Ontheway •
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Ontheway •
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One approach...
Use IPR scan to get GO terms for your proteins. GO annotations should contain information regarding biological function.
Basically you want GO terms. There are a couple ways to get there.
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Just bear in mind that no computational method can "tell whether a protein is involved in a secretion system." Only experimental validation can do that. However, bioinformatics can make useful predictions.