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This week€™s addition to the virology toolbox was written by Chris Upton (Disclaimer: BBB was developed in the Upton lab, so this is a biased review.) This will be a multi-part posting describing the key features of BBB. Base-By-Base (BBB) is a Java (platform independent) multiple sequence alignment (MSA) editor. Development was begun many years …

Viral bioinformatics: Multiple sequence alignment €“ Base-By-Base (BBB) editor Read More »

This week€™s addition to the virology toolbox was written by Chris Upton Generating multiple sequence alignments (MSA) is one of the most commonly used bioinformatics techniques. The sequences to be compared can be DNA (promoters, genes, genomes) or proteins. Note that the length and number of sequences to be aligned has an impact on the …

Viral bioinformatics: Introduction to multiple sequence alignment Read More »

I arrived in Munich, Germany today for the start of a Symposium entitled ‘Viral offense and immune defense’. It is organized by Collaborative Research Center 455 (in German, Sonderforschungsbereich, SFB 455); these are centers funded by the German Research Foundation that support collaborative research throughout the country. This meeting will highlight 21 internationally renowned speakers …

Munich Symposium: Viral offense and immune defense Read More »

This week€™s addition to the virology toolbox was written by Chris Upton Dotplots are an extremely useful way of visualizing comparisons of small and large DNA sequences (as well as protein sequences), providing insight into the degree of similarity, deletions, insertions and direct and indirect repeats. In a dotplot, each nucleotide, or small window of …

Viral bioinformatics: Dotplot Read More »

If there€™s something strange in your neighborhood, who you gonna call? EIS! In the early 1950s, Alexander Langmuir, an epidemiologist for the Communicable Disease Center (CDC) in Atlanta, Georgia, warned that pathogenic microbes could be used as agents of biological warfare. To counter the threat, he advised the federal government to establish a ready response …

Inside the outbreaks Read More »

This week’s addition to the virology toolbox was written by Chris Upton First, you may be asking yourself €“ Why viral bioinformatics? Good question! Although it€™s true that much in the world of bioinformatics can be applied to all manner of protein and DNA sequences, there are a number of resources that are specific for …

Viral bioinformatics: Introduction + Homology Read More »