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Understanding genomic information: A short discussion of protein bioinformatics and the role of the internet in enhancing the process: 

July 7, 2000 1 Patricia Babbitt, PhD Univ. of Calif., San Francisco Understanding genomic information: A short discussion of protein bioinformatics and the role of the internet in enhancing the process

Now that the genome is “done,”what do we do with it?: 

July 7, 2000 2 Patricia Babbitt, PhD Univ. of Calif., San Francisco Now that the genome is “done,” what do we do with it? Identification of genes associated with health, disease, a better understanding of biology Tracing cell circuitry Prediction of function/other characteristics for the protein products of the genes - drug discovery - agriculture - protein engineering/biocatalysis

Slide3: 

July 7, 2000 3 Patricia Babbitt, PhD Univ. of Calif., San Francisco But prediction of protein functional characteristics can be very difficult...

Slide4: 

July 7, 2000 4 Patricia Babbitt, PhD Univ. of Calif., San Francisco Sequence Conservation Structure Conservation Function Conservation

Critical roles for the Internet in protein informatics research: 

July 7, 2000 5 Patricia Babbitt, PhD Univ. of Calif., San Francisco Critical roles for the Internet in protein informatics research Archiving, dissemination of sequence/structural/functional information Development, dissemination of tools Pre-computing some of the answers Hot links

Archiving & dissemination: 

July 7, 2000 6 Patricia Babbitt, PhD Univ. of Calif., San Francisco Archiving & dissemination Massive public databases: Genbank (NIH) No access to proprietary databases How to integrate experimental information from high-throughput methods? How to evaluate, link, update and fund secondary databases of critical information? Enzyme mutations, information from mass spectrometry, protein structural classifications, descriptions of metabolic pathways, class-specific sites

Development, dissemination of tools: 

July 7, 2000 7 Patricia Babbitt, PhD Univ. of Calif., San Francisco Development, dissemination of tools Primary database search/analysis tools available via remote servers BLAST, multiple alignment algorithms, motif finding, structural comparison Source code/technical support available for some tools

Development, dissemination of tools, cont’d: 

July 7, 2000 8 Patricia Babbitt, PhD Univ. of Calif., San Francisco Development, dissemination of tools, cont’d On-line directories provide enhanced access to specialized tools Training comes with the package Rasmol, BLAST tutorials, phylogenetic analysis But simple tutorials may greatly oversimplify the problem of understanding how to do research with those tools

Pre-computing some of the answers: 

July 7, 2000 9 Patricia Babbitt, PhD Univ. of Calif., San Francisco Pre-computing some of the answers Preliminary functional analysis performed during archiving of new ORFs Error rate is unknown, impossible to catch using automated methods, and the consequences could be substantial Many other important characteristics are included in the primary archive MW, length, gene name, species of origin, family/superfamily to which it belongs, specific functional characteristics when known, primary references

Pre-computing more of the answers: 

July 7, 2000 10 Patricia Babbitt, PhD Univ. of Calif., San Francisco Pre-computing more of the answers Pre-computed analysis of “higher order” value: e.g., protein families, motifs, structural classifications Pfam, Systers, Prints, ProDom, Metafam, Prosite Quality is highly variable; different sites sometimes have different answers Other primary sites now on-line and often linked to master databases such as Genbank E.C. classifications, genome project centers, IUPAC/IUBMB nomenclature

Hot links: 

July 7, 2000 11 Patricia Babbitt, PhD Univ. of Calif., San Francisco Hot links NIH’s Entrez and other linked systems: moving close to the goal... Genbank n Medline n OMIM n PDB n tools n COGS Many individual academic or government sites also provide good hot links or “see also lists” Updates a constant problem Search engines still inadequate