Category Archives: bioinformatics

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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