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

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Presentation transcript:

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

TC vs. EC Transport commission Homologous proteins go together Transport Classification (TC) page Enzyme commission Homologous proteins not necessarily go together International Union of Biochemistry and Molecular Biology (IUBMB) nomenclature page

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

PSI Blast – Xylella proteins CorrectWrong A B C % over total of 2830 proteins

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

Acknowledgments FAPESP Ludwig Institute / Butantã Foundation CNPq