Category Archives: annotation

Last session of annotation: using literature, KEGG, Blast and UniProt (mostly)

Following last week’s summary of some student annotation topics, here are some more. I didn’t have time to interview all the students, so some topics were not yet covered, and some only very rapidly, but it gives an idea of … Continue reading

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Update on annotation of Pseudomonas protegens: confirmations and surprises #biocuration

After 2 weeks of annotation, some of our students presented their preliminary results to the class. Here is a summary. Phosphate and nitrate uptake and metabolism: using KEGG and keywords, the students identified genes to annotate; of these, 45 have … Continue reading

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Starting annotation of the P. veronii genome #biocuration

After completing genome assembly (see previous blog post), our students have now started 4 sessions of annotation. They have chosen among 15 proposed topics, of interest either for all bacterial genomes, or specifically to this isolate from a solvent-contaminated soil. … Continue reading

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Annotating Ralstonia genomes: what have our students been up to? #biocuration #bioinformatics

Last week of annotation by our students (see list of annotation topics). Let’s see what they’re up to. This is a snapshot of an unfinished annotation. In which of the three replicons are the core genes? And first, are they … Continue reading

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Annotating two genomes #biocuration

The students have started annotating the two best genomes from the assembly. For this, most of them are using the GenDB platform to annotate specific systems: Secretion systems; Transporters; Prophages and genomic islands; Aromatic compound metabolism; alternative respiration; Replicons; N-fixation … Continue reading

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Highlights of our annotation: heavy metal resistance, lateral gene transfer, genomic islands, mega plasmids!

This was the last day of annotation for our students, where they had to write up their results. Next week, oral presentations of the results. In the meantime, I asked each group of 2 or 3 students for some highlights … Continue reading

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Bacterial genome annotation strategies

Into our third week of genome annotation, a look at the strategies of different student pairs. In all of these, annotation is still ongoing. Integrated phages and genomic islands: Neochlamydia: No results with PHAST. 🙁 GC-skew confirmed the order of … Continue reading

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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.) … Continue reading

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