Video Tips of the Week: Annual Review IV, 2nd half

… key sequence variations

December 14: Big changes to NCBI’s genome resources

December 21: eggNOG for the Holidays (or to explore orthologous genes)

December 28: Video Tips of the Week: Annual Review IV (first half of 2011)

Video Tip of the Week: eggNOG for the holidays (or to explore orthologous genes)

Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December.

Oh, that’s not what this tip is about, it’s about database of orthologous groups of genes, eggNOG. We’ve mentioned eggNOG before …

NAR database issue (always a treasure trove)

… to my former PI at EMBL because I can, Peer Bork’s group has 4 databases listed in the issue: eggNOG, SMART, STITCH and OGEE. (and he and a couple members are on the InterPro paper also).

This is going to be a wealth of information to wade through!

UCSC Genome Browser: http://genome.ucsc.edu

Ensembl: http://www.ensembl.org/

UniProt: http://www.uniprot.org/

MINT: http://mint.bio.uniroma2.it/mint/

SMART: http://smart.embl.de/

WormBase: http://www.wormbase.org/ …

Tip of the Week: MetaPhoOrs, orthology and paralogy predictions

… available in seven popular homology prediction services ( PhylomeDB,  EnsemblCompara,  EggNOG,  OrthoMCL,  COG,  Fungal Orthogroups, and TreeFam ).

The research article on their methodology published in NAR (online 12/10) will give you a better understanding how these orthology and paralogy predictions are made. Basically, MetaPhOrs uses phylogenetic orthology and paralogy predictions from several sources. These phylogenies overlap:

Since many of these repositories …

Liveblogging the GenBank 25th Anniversary II

… (Tatusov, Koonin, Lipman). Sci 278:631. Clusters of orthologous genes. Slide w update of COGs (eggNog) NAR 2008 36:D250. Slide of COGs in glycolysis.

Larger scale picture of evolution becomes possible: 1997 Koonin et al. Mol Microbiol 25:619. Soon after gene exchange in bacteria/archae Trends Genet: 1998 Aravind et al.

Illustrates work on NO receptor, Iyer et al 2003 BMC Genomics. Brochier et al paper on horizontal transfer Trends Genet 2000. Car analogy for swapping parts. (What is …