Koonin

RL Tatusov, EV Koonin, DJ Lipman. A genomic perspective on protein families. Science 278 631-637, 1997. 

Koonin, E. V., et al., 1996. Sequencing and analysis of bacterial genomes. Current Biology 6 404-416. 

Subramanian G, Koonin EV, Aravind L. Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. Infect Im-mun 2000 68(3] 1633-1648. 

Aravind L, Dixit VM, Koonin EV. Apoptotic molecular machinery vastly increased complexity in vertebrates revealed by genome comparisons. Science 2001 291[5507] 1279—1284. 

Fig. 2.12. 5-factor for 12C(a, y)lsO. The dashed curve ignores the sub-threshold resonances, while the continuous curve allows for them, but the uncertainties are still significant at low energies. Koonin, Tombrello and Fox (1974). Reproduced with kind permission of Elsevier Science. Courtesy S.E. Koonin. 

The second postprocessing step is the automated enhancement of the TrEMBL annotation to bring TrEMBL entries closer to SWISS-PROT standard. There is an increasing need for reliable automatic functional annotation to cope with the rapidly increasing amount of sequence data. Most of the current approaches are still based on sequence similarity searches against known proteins. Some groups try to collect the results of different prediction tools in a simple way, e.g., PEDANT (Frishman and Mewes, 1997) or GeneQuiz (Scharf et al., 1994). However, several pitfalls of these methods have been reported (Bork and Koonin, 1998). 

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