hello everyone!
i got a question to ask you guys.recently our lab focused on a type of secreted protein to predict and its identification,then i searched the related articles then i found the paper titled
Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000
(http://www.pnas.org/content/99/11/7652.short)
in this paper, the author used software Artemis to predict the secreted effector. i never used this type of software before and so do the other guys in our lab,after times and times of trial i still didn't know how to use it.
could you please help me out with it, step by step.
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written
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User 5570 •
1 answer
The paper method section list the software used. You should read up about them on their websites. Artemis is a genome browser and annotations viewer. It doesn't do any heavy analysis, just visualization. They annotated the genome using Lasergene's DNAStar program with the prosite motif described in the methods.
DNAStar is a commercial software. It looks like they probably used the Genequest module for the gene finding: http://www.dnastar.com/t-sub-products-lasergene-genequest.aspx
If you want a free open source way to scan sequences using prosite motifs, you can read about prosite and download their scanning software: http://prosite.expasy.org/
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written
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Damian Kao
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