Starting to annotate our two genomes

We have now started annotating our two genomes with our students. We use GenDB, a semi-automated system which provides a first run of automatic annotations, and integration of results from many bioinformatics analyses (BLAST against various databases, trans-membrane domains, etc.) as well as a genome browser and an interface to KEGG.

Our Neochlamydia and our Ralstonia have never been sequenced before, but we know where we found them, and we know related genomes, which gives us some clues to their biology. The Ralstonia was isolated from a contaminated groundwater aquifer. The Neochlamydia was also isolated from the environment, and both might have heavy metal resistance for example.

The students are now grouped in pairs (and one trio), and are annotating different sub-systems using GenDB as well as information from outside resources, such as StringDB. The systems are:

•Amino acid biosynthesis
•Transporters
•Conservation of the type III secretion system
•Prophages & genomic islands
•CRISPR elements
•Carbon metabolism
•Mobile genetic elements (ICE, Tn) and prophages
•Replicons
•Respiration and N-metabolism

This process of annotation will take us four 4 hour sessions (we’re half way through!). Each annotation goes through the steps of automated annotation, suggestion by a student, verification by a teacher who provides feed-back, final annotation by a student, and validation by a teacher. In the process, we learn more about these bacteria, and the students learn about the labor-intensive process of manual curation of biological data. And since none of the teachers knows everything from microbiology to bioinformatics, we all learn to be better genome biologists.

We will update this blog with the results of the annotation process.

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