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SRI International Bioinformatics 1 Navigation to Related Objects Bioinformatics Research Group SRI International Mario Latendresse.

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Presentation on theme: "SRI International Bioinformatics 1 Navigation to Related Objects Bioinformatics Research Group SRI International Mario Latendresse."— Presentation transcript:

1 SRI International Bioinformatics 1 Navigation to Related Objects Bioinformatics Research Group SRI International Mario Latendresse October 2010, Pathway Tools Workshop

2 SRI International Bioinformatics 2 Available on the Web Applies for compounds, genes, proteins, reactions, pathways Once such an object is found, a new menu appears on the right on the top menu bar The menu offers to search the object found: 1. In all databases or 2. Another database The In all databases is demanding (BioCyc has over 1000 databases); more so for genes and proteins

3 SRI International Bioinformatics 3 Does this Object Exist in Other PGDBs?

4 SRI International Bioinformatics 4 How is Similarity Computed? For pathways, reactions, and compounds: based on frame-ids (unique identifiers) For proteins and genes: based on names, synonyms, and orthologs l The result page tells you, for each database, if found based on name/synonyms or orthologs, or both

5 SRI International Bioinformatics 5 Demo on the Web of another database 1. At BioCyc.org, select E. coli K12 as the database to search 2. Search for the glycolysis pathway using the Search->Pathways command 3. Once the glycolysis pathway is displayed, Select the command Pathway->Show this pathway in another database 4. Select the database to search (e.g., MetaCyc) 5. If it exists in the other database, the glycolysis pathway is displayed for this database

6 SRI International Bioinformatics 6 Demo on the Web of in all databases 1. At BioCyc.org, select E. coli K12 as the database to search 2. Search for compound N-methyltryptophan. 3. Once the compound is displayed, select the command Compound->Show this compound in all databases 4. About 28 databases (the number depends on the current version of BioCyc.org) are found containing that compound

7 SRI International Bioinformatics 7 Result for In all databases for a Compound

8 SRI International Bioinformatics 8 For Genes and Proteins The search for similar proteins and genes is based on names (name and synonyms) and orthologs The result page gives the reasons of the match

9 SRI International Bioinformatics 9 Result In all databases for a Gene

10 SRI International Bioinformatics 10 Implementation The two commands are implemented using BioVelo. A general purpose query language for Pathway Tools The query itself can be saved since it appears as a URL in the browser

11 SRI International Bioinformatics 11 Implementation (2) Searching all databases for a pathway [ ( Z1,r ): Z1<-dbs, r := Z1~GLYCOLYSIS ] Searching all databases for a compound [ (Z1,r,r^Chemical-formula): Z1 <- dbs, r:=Z1~PEPTIDE-TRYPTOPHAN ] Searching all databases for a reaction [ (Z1,r,r^EC-number): Z1 <- dbs, r := Z1~L-IDITOL-2-DEHYDROGENASE-RXN ] Searching all databases for a gene [ r : l1 := find-objects(META,ECOLI~EG11024), l2 := find-orthologs(META,ECOLI~EG11024), both := l1**l2, ort := l2 -- both, sim := l1 -- both, r <- … both … ort … sim …]

12 SRI International Bioinformatics 12 Navigation to Related Objects Questions?


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