Question: Schmidtea mediterranea annotation problems
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gravatar for kalmeshv83
9 months ago by
kalmeshv830
kalmeshv830 wrote:

I am doing RNA-Seq analysis of Schmidtea mediterranea(fresh water planaria). The major problem is annotation. How do I get any useful gene data from the up and down regulated hits that I got (or just assuming I have a subset of "mkids"). I used annotation files from the Smed database which has only gene predictions(from maker) and the annotation from wormbase has only "mk" ids . I have used genomes from worm base and SmedDB.Also how can I get GO enrcihment and pathway enrichment for the hit genes(mkids or maker gene predictions)?

sequencing rna-seq gene genome • 249 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by kalmeshv830

You could obtain GO-terms by blasting against UniProt and using hmmer against Pfam. Maybe eggnog (http://eggnogdb.embl.de/#/app/home) could be of use?

ADD REPLYlink written 9 months ago by cschu1811.4k

Thanks. Do you know how i can get the actual genes from the maker gene predictions?I know I can get the gene sequence and then blast it and know the gene but how do I do it for all genes at once?

ADD REPLYlink written 9 months ago by kalmeshv830
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