The free Polyidus software identifies the exact genomic regions for integration of a known virus. We developed Polyidus to identify viral integration sites with chimeric sequencing reads from any paired-end sequencing data. First, Polyidus aligns reads to a viral genome. It allows for partial mapping using local alignment, and removes any sequencing fragment where neither read maps to the virus. Second, Polyidus aligns the selected reads to the host genome, permitting partial mapping. Third, Polyidus identifies chimeric reads: those reads mapped partially to the host genome and partially to the virus genome. Fourth, for each chimeric read, Polyidus reports the start and strand of integration in both the host and viral genomes. Polyidus also reports the number of chimeric reads supporting each integration site. [more inside]
I have assembled tables of COVID-19 virus data using the daily reports from each state of the United States. From this database of approximately 20,000 entries, I have assembled weekly statistics and rankings for each state. [more inside]
The purpose of this blog is to share our appreciation for the study of microbial viruses, the viruses that infect Eubacteria (also known as bacteriophage), Archaea, and microbial Eukaryotes. They dominate our planet's ecosystem, serve as a profoundly useful model system for understanding life at its simplest, possess a dizzying array of powerful molecular tools we can borrow, and make steadfastly vicious allies in our fights with problematic microbes. Our name is based on the nursery rhyme "The Siphonaptera," which eloquently describes a beautiful phenomena found more clearly in the viruses that infect microbes than anywhere else.
Big fleas have little fleas,
Upon their backs to bite 'em,
And little fleas have lesser fleas,
and so, ad infinitum.
And the great fleas, themselves, in turn
Have greater fleas to go on;
While these again have greater still,
And greater still, and so on.