If I’m only going to write one or two blog posts a year on this blog, then it makes sense to return to my recurring theme of don’t use CEGMA, use BUSCO! In 2015 I was foolishly optimistic that the development of BUSCO would mean that people would stop using CEGMA — a tool that we started developing in 2005 and which used a set of orthologs published in 2003! — and that we would reach ‘peak-CEGMA’ citations that year. That didn’t happen. At the end of 2017, I again asked the question have we reached peak-CEGMA? because we had seen ten consecutive years of increasing publications. Well I’m happy ..read more

These days, I mostly think of this blog as a time capsule to my past life as a scientist. Every so often though, I’m tempted out of retirement for one more post. This time I’ve actually been asked to bring back my JABBA awards by Martin Hunt (@martibartfast)…and with good reason! There is a new preprint in bioRxiv… CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning I’m almost lost for words about this one. You know that it is a tenuous attempt at an acronym or initialism when you don’t use any letters from the 2nd, 3rd, 4th, or 5th words of the full sof ..read more

A new tool, recently published in Nucleic Acids Research, caught my eye this week: DOGMA: a web server for proteome and transcriptome quality assessment The tool, by a team from the University of Münster, uses protein domains and domain arrangements in order to assess 'completeness' of a proteome or transcriptome. From the abstract… Even in the era of next generation sequencing, in which bioinformatics tools abound, annotating transcriptomes and proteomes remains a challenge. This can have major implications for the reliability of studies based on these datasets. Therefore, quality assessment ..read more