Author Archives: Marc Robinson-Rechavi

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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Good assembly of genomes with #PacBio: no difference between our strains

A new year of the class Sequence a genome with our master students has started! In September, the students cultivated two strains likely to be Pseudomonas protegens, extracted their DNA and prepared it for PacBio sequencing. All of the students … Continue reading

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#Bioinformatics treatment of bacterial #RNAseq data

The students of the Sequence a genome class have been advancing in their analysis of bacterial RNA-seq (see design in previous post). Let’s present here the basic analysis, common to all biological questions which can then be studied using these … Continue reading

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Experimental preparation of #RNAseq samples

This winter, the Master students preformed the experimental part of our RNA-seq. This blog is a bit late, so they have in the meantime started the bioinformatics analysis, which will be reported in a future blogpost (hopefully less late than … Continue reading

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Second paper from the Sequence a genome class published

After a first paper in June last year, a second paper from our class of sequencing, assembling and annotating bacterial genomes with Master students is out: Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students … 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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Finishing PacBio assembly, and a presentation by our local PacBio representative

In this first session of the course “Sequence a genome” since we sent DNA to the sequencing facility, we have had the visit of Gerrit Kuhn, who supports PacBio in our area, and who gave a nice presentation of how … Continue reading

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A new adventure: PacBio sequencing and RNA-seq in the classroom

This class has been running since 2010-11, on the following principle: autumn semester: isolate bacterial DNA, sequence using Illumina, assemble; spring semester: close assembly gaps, annotate genome. As anyone following genomics knows, the times they are a’changing again and again, … Continue reading

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Our first student genome paper is out: Miyazaki et al Environ Microbiol

The first paper describing a genome sequenced, assembled and annotating by students in our course, which was accepted in April (that blogpost includes the full list of authors with student names in bold), is now online: Comparative genome analysis of … Continue reading

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