The Analytic Garden

We have been informed today, in addition to spreading more quickly, it also now appears that there is some evidence that the new variant - the variant that was first identified in London and the South East - may be associated with a higher degree of mortality ~ Boris Johnson It's all going to be about the [COVID-19] variants and the vaccine, and that will determine where we're going to be next year, the year after, and the year after that. ~ CBS, Mar 12, 2021 The Covid-19 variant B.1.1.7 , aka the UK variant has been making news for the last few months. B.1.1.7 is estimated to be 40%–80% more transmissible than wild-type SARS-CoV-2 and was detected in the UK in November 2020 from a sample taken in September. I wanted to take a look at its development so I downloaded the latest data from GISAID  on March 18, 2021. The data included a tab delimited meta file containing 769,387 observational rows of 28 variables. The first things I wanted to look at was the time course of th...

Data is the new science. Big Data holds the answers. ~ Pat Gelsinger A strong feeling of adventure is animating those who are working on bacterial viruses, a feeling that they have a small part in the great drive towards a fundamental problem in biology. ~ Max Ludwig Henning Delbrück Since about this time last year, I have been tracking mutations in the Sars-CoV-2 virus. I have mostly been relying on data from NCBI . Right now, the NCBI database contains 51,650 Sars-CoV-2 genomic sequences. On a well-powered desktop computer, it's possible to analyze that amount of data, albeit slowly. However, the major depository of pandemic sequences is at GISAID . At this point, GISAID contains over 500,000 genomic sequences. Dealing with that amount of data on a desktop system presents some new problems. On Jan. 27, 2021 I downloaded a multiple sequence alignment from GISAID. It contained 399,796 sequences, each with 32,280 letters. The MSA file weighs in at about 13 Gb. The first thing I want...