phylogeny

Talk for Metagenomics Conference

Today's tip for the week is a quick introduction to PhylomeDB, gene phylogenies database. Read more information about this database at the OpenHelix Blog

Our latest weekly tip on the Interactive Tree of Life, iTOL. You can find out more at our blog

A quick introduction to a genome evolution, syteny and gene duplication visualization tool. For a higher-resolution, http://blog.openhelix.eu/?p=3916

The endophytic lifestyle has played an important role in the evolution of the morphology of reproductive structures (body) in one of the most problematic groups in fungal classification, the Leotiomycetes (Ascomycota). Mapping fungal morphologies to two groups in the Leiotiomycetes, the Rhytismatales and Hemiphacidiaceae reveals significant divergence in body size, shape and complexity. Mapping ecological roles to these taxa reveals that the groups include endophytic fungi living on leaves...

Biological network alignment.

Further details of the book can be found at http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470181052.html and on Google Books http://books.google.com/books?id=4H_ai7ivRIcC&pg=PP1&dq=structural+bioin... .

The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Despite this variation in complexity, all the proteasomes are composed of homologous subunits. We...

The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world. On more than 9000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics. See: http://www.tolweb.org/

A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides the 174 taxa into Archaea, Bacteria, and Eukarya and satisfactorily sorts most of the major groups within these superkingdoms. The most challenging problem involved 119 Bacteria, many of which have reduced genomes. When a weighting factor was used that takes account of difference in genome size...