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Automatic Annotation of Transport Proteins M. Braga Lin T. L. J. Meidanis

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1 Automatic Annotation of Transport Proteins M. Braga Lin T. L. J. Meidanis http://cancer.lbi.ic.unicamp.br/

2 TC vs. EC Transport commission Homologous proteins go together Transport Classification (TC) page http://www.biology.ucsd.edu/~msaier/ Enzyme commission Homologous proteins not necessarily go together International Union of Biochemistry and Molecular Biology (IUBMB) nomenclature page http://www.chem.qmw.ac.uk/iubmb/

3 Benchmark Xylella fastidiosa transport analysis 2830 proteins Meidanis, Braga, Verjovski-Almeida (2002), Microbiology and Molecular Biology Reviews, to appear.

4

5 PSI Blast – Xylella proteins CorrectWrong A65.934.1 B92.47.6 C91.88.2 % over total of 2830 proteins

6 Why algorithm B errs Ntops smaller than needed – role? Misses family, gets superfamily No convergence in PSI-BLAST Same example in more than one family

7 Acknowledgments FAPESP Ludwig Institute / Butantã Foundation CNPq http://cancer.lbi.ic.unicamp.br/

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