Sunday, 17 January 2016

Uncultured bacterial majority? Digitally unannotated majority of the minority is worse

Aquifex, an exiting bacterium, which unexciting BioSample data.
It has been remarked that the majority of bacterial diversity remains uncultured. A fraction of the cultured bacteria are genome-sequenced and a fraction of these have an machine-readable data about them.

Saturday, 16 January 2016

The contagious ORF annotation error of 16S rRNA

Some time back in many genomes there were a few copies of a small hypothetical open reading frame, sometimes annotated as a quinone oxidase. These organisms also had less 16S rRNA than 23S rRNA. This is not some curious observation about enzyme evolution of a duo of a promiscuous ribozymatic activity of 23S rRNA and small protein that could lead to a Nature paper, though. In reality it is a sequence annotation error that seems quite viral in NCBI.

Getting the corresponding nucleotide sequences of protein sequences

Getting stuck on a really simple task is not a nice feeling.
A seemingly simple challenge I have faced a few times so far is getting the nucleotide sequence corresponding to a protein sequence: this seems really straightforward, yet it is not.