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International Summer School
From Genome to Life:
Structural, Functional and Evolutionary approaches
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BRENNER
Steven |
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University of California, 461 Koshland Hall, #3102, Berkeley, CA 94720-3102 title: Challenges in genome annotation Functional description of the complete repertoire of proteins encoded by a genome lies at the core of genomic biology. In general, one accepts genome sequence, gene predictions, and gene annotation as reliable sources from which biological inferences may be drawn and further experiments devised. However, computational functional characterization is fraught with challenges and the ultimate result is often of questionable reliability. In this session, I will review the typical steps in genome annotation, indicating which steps are reliable and which remain a challenge. We will make a case study of the annotation of M. genitalium, where multiple groups’ annotations provide us with the ability to gain some measure of the accuracy of genome annotation. A second case study will explore a set of proteins which are both transmembrane and transcription factors, as an example of the incredible challenge of making meaningful functional predictions. The session will conclude with discussion of approaches that may make functional annotation more reliable and valuable. References (available at http://compbio.berkeley.edu/people/brenner/pubs/):
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BRENNER
Steven |
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University of California, 461 Koshland Hall, #3102, Berkeley, CA 94720-3102 title: Structural genomics of proteins and RNA Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. In this session, I will begin by outlining the basic principles underlying structural genomics. Methods to be discussed include target selection and structure analysis. I will review the classifications used to analyze solved protein and RNA structures. I will review progress from structural genomics to date and provide an outline of expectations for structural genomics. References (available at http://compbio.berkeley.edu/people/brenner/pubs/):
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