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Searching BioCyc Ron Caspi 1 SRI International Bioinformatics Help is One Click Away! 2 SRI International Bioinformatics The Web Account System 3 SRI International Bioinformatics The Web Account System Creating a web account enables you to: Save Object Groups Define page formatting preferences Define Overview layout preferences Save organism groups for comparative analysis 4 SRI International Bioinformatics Save Organism Groups with Web Accounts 5 Note the My Lists tab on the multi-organism selector for comparative analyses. When you perform comparative analyses, you can easily save groups of organisms for re-using at a later time. SRI International Bioinformatics Define a Favorite Database with Web Accounts If you create a web account, you can define a favorite database that will be opened by default when you login 6 SRI International Bioinformatics Searching 7 SRI International Bioinformatics Why the Need for Dedicated Search Tools Search BioCyc for “L-arginine” 2080 results Need to have specific tools for finding exactly what we search for. 8 SRI International Bioinformatics BioCyc Searches 9 Multiple searches available for finding information in different ways The easiest searches to use are fairly coarse Start by selecting database to search Simplest search: Quick Search At upper right of most pages SRI International Bioinformatics Selecting the Database You can only search one database at a time*! * With the exception of Google searches Click on word “change” under Search menu or under Quick Search button In resulting selector, choose a PGDB 10 Start typing a word in organism name Click on letter to navigate to organisms starting with that letter Click a frequently used PGDB Select by Taxonomy All subsequent searches will apply to that database SRI International Bioinformatics The Quick Search Box 12 What can you type here: Gene names (dnaA ) Compound name (L-lysine) Pathway name (peptidoglycan biosynthesis) Reaction name (lysine decarboxylase) Protein name (peptidase) EC number (1.3.1.26) Organism name (Escherichia coli) Frame ID (CPLX-8024) GO term (0006086) Links to other databases (O33998) An exact term using the format (Peptidase D search:exact) Limited term (hydrogen type:compound) What doesn’t work: Exact text using the Google format (“peptidase D”) SRI International Bioinformatics Quick Search Results Results are divided into multiple categories 13 SRI International Bioinformatics Examples of searches performed by users of the BioCyc website: Successful Ascorbate EC 3.4.17.5 Sigma factor Polysulfide reductase Entner-Doudoroff pathway Cyanobacteria DnaA Unsuccessful pheV Transmembrane helix 6 3.4.24.B11 ABC cobalt transporter affinity of DnaA A simple auto-correction mechanism tries to correct typos. For example, searching for “sacrosine” will find “sarcosine”. 14 SRI International Bioinformatics Quick Gene Search Useful when only interested in genes. For example, compare the results when searching for “dnaA” by using the Quick Search and Gene Search buttons. 15 SRI International Bioinformatics The Search Menu 16 Search Menu Object-specific searches Advanced search Ontologies search Google search BLAST search Search of full-text articles (EcoCyc only) SRI International Bioinformatics Google This Site The BioCyc site is indexed by Google You can launch a Google text search from: 1. Search → Google This Site 2. The alternative searches box that appears on Quick Search results pages 17 SRI International Bioinformatics Object-Specific Searches The first four items in the search menu provide a medium-level search interface against single types of objects Use of filtering 18 Click on triangles at the left to expand or hide filters Note that if a filter is hidden it will not be used in a search SRI International Bioinformatics Compound Search All buttons – quick way to get complete lists Examples for compound searching: List 19 SRI International Bioinformatics Search Genes/Proteins/RNAs All buttons – quick way to get complete lists Extensive filtering options List 20 SRI International Bioinformatics Search Pathways 21 SRI International Bioinformatics Advanced Search The BioVelo query language SAQP: Structured Advanced Query Page Permits the definition of complex searches without mastering BioVelo. To learn more about the advanced query interface, see online documentation. 22 SRI International Bioinformatics Sequence Search by BLAST unusual here – a regular BLAST interface that permits BLASTing sequences against BioCyc PGDBs. The results are linked to the PGDB gene/protein pages Nothing 23 SRI International Bioinformatics Growth Media and Phenotype 24 The desktop version of Pathway Tools allows definition of growth media, gene knockout growth information, and growth data for phenotype microarray plates. SRI International Bioinformatics EcoCyc-Specific Searches: Growth Media Search for growth media based on: name compounds present compounds not present observed growth 25 SRI International Bioinformatics EcoCyc-Specific Searches: Textpresso 26 Mining E. coli literature poses special challenges – because almost every molecular biology paper references E. coli The solution – EcoCyc Textpresso! An E. coli only collection of literature 30,000 full-text articles and 6,500 abstracts. Full text literature searches Results presented at bottom of page SRI International Bioinformatics