Category Archives: students

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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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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Closing the assembly #bioinformatics

We left you with assemblies numbering tens of contigs. The next step was for our students to order them. We chose to go ahead only for strains 705 and 743. For strain 705 we had an optical map to help … Continue reading

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Progress in genome assembly: 3 strains, 6 QC parameters, 3 software, 2 k-mers #bioinformatics

Restarting this blog after a pause due to other duties, extra motivated by the acceptance of our first paper… This autumn, our students worked hard to make their millions of reads into assembled genomes. The students have worked on a … Continue reading

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How do our students feel after two semesters of genome sequencing?

I interviewed our students on the last day of annotation on their impressions and take-home message from the two semesters of this class, from extracting the bacterial DNA to summarizing their annotation of a specific subset of the genome. The … Continue reading

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