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 several times, but only in passing or in relation (orthologous? ) to another database or tool. Today, in perfect timing for the season, thought I’d do a quick tip to introduce eggNOG.
eggNOG is brought to you by the same research group that developed a lot of other excellent tools such as SMART (protein domains), STRING (protein-protein interactions, STITCH (protein-chemical interactions) , iTOL and so much more. Of course they do some fascinating research too.
eggNOG is a relatively straightforward database to use, but it has a wealth of information you might want to check out. As the recent paper in NAR states:
Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses…. Orthology, defined as homology via speciation, is a crucial concept in evolutionary biology and is essential for disciplines such as comparative genomics, metagenomics and phylogenomics. The concepts of orthology and paralogy, with the latter being defined as homology via duplication, have been used as a foundation to introduce the concept of clusters of orthologous groups: proteins that have evolved from a single ancestral sequence existing in the last common ancestor (LCA) of the species that are being compared, through a series of speciation and duplication events. Orthologous groups (OGs) have proven useful for functional analyses and the annotation of newly sequenced genomes as orthologs tend to have equivalent functions.
721 801 orthologous groups, encompassing a total of 4 396 591 genes…. from 1133 species.
For more about orthologous groups, methods used and pros and cons of methodology, you might want to check out the paper referenced below. They’ve included several informative and helpful reviews and references.
Right now, take a quick tour of what eggNOG can offer.
Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L., von Mering, C., & Bork, P. (2011). eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges Nucleic Acids Research DOI: 10.1093/nar/gkr1060