Bioinformatics as a Tool

The complete genomes of a handful of plant and plant-like algal species— Arabidopsis thaliana (AGI2000), Oryza sativa (Goff et al. 2002; Yu et al. 2002), Populus trichocarpa (Tuskan et al. 2006), Ostreococcus tauri and lucimarinus (Derelle et al. 2006), and Cyanidioschyzon merolae (Matsuzaki et al. 2004)— have been published; the genomes of Medicago truncatula (a relative of alfalfa), the moss Physcomitrella patens, the club-moss Selaginella moellendorf-fii, the algae Chlamydomonas reinhardtii, Volvox carteri, Galdieria sulphu-raria and others are well on their way. Keeping in mind that genes can diverge considerably without losing function and that some conserved proteins have very different functions across species, we can nonetheless ask what TOR signaling components are present in plant genomes. To do this, one need only to blast (Altschul et al. 1997) the Arabidopsis or other plant genome with the protein of interest, and then verify the plant hit by blasting it against the genome of the organism encoding the probe protein; if the strongest hit is to the original probe protein, one can safely conclude that the hit is indeed a homologue.

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