1 / 18

Introduction to the Pathway Tools Software

Introduction to the Pathway Tools Software. David Walsh and Simon Eng bigDATA Workshop—May 29, 2010. Outline. Metabolic annotation from genomic data Pathway Tools and MetaCyc facilitated genome /pathway annotation Pathway/genome database (PGDB) exploration

lilike
Download Presentation

Introduction to the Pathway Tools Software

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Introduction tothePathway Tools Software David Walsh and Simon Eng bigDATA Workshop—May 29, 2010

  2. Outline • Metabolic annotation from genomic data • Pathway Tools and MetaCycfacilitatedgenome/pathway annotation • Pathway/genome database (PGDB) exploration • Potential applications in environmental ‘omics

  3. ?!?!

  4. Metabolic Annotation Workflow Pathway Tools Automated Manual

  5. Pathway Tools is a software suite for workingwith pathway/genome databases http://bioinformatics.ai.sri.com/ptools

  6. Pathway/Genome Databases (a.k.a. PGDBs) integrate genomic data withdetailed functional annotations (including metabolic pathways)

  7. The Three Tiers of PGDBs

  8. MetaCyc is a continuously curated PGDB of 1400+ reference pathways from 1800+ organisms encompassing all domains of life http://www.metacyc.org

  9. MetaCyc Statistics by Year Adapted from http://www.metacyc.org/release-notes.shtml

  10. Novel metabolic pathways can be created at will in Pathway Tools (PGDBs are therefore dynamic)

  11. PathoLogic predicts metabolic pathways in a PGDB based on reference PGDBs

  12. PathoLogic reads GenBank and nucleotide FASTA files (but it also has a native file format)

  13. PathoLogic infers metabolic pathwaysfrom functional annotations Product names EC numbers GO terms

  14. PathoLogic applies an iterative algorithm that keeps track ofcandidate and undecided pathways

  15. How PathoLogic Works

  16. Demonstration on two rRNA-containing fosmids ofan uncultivated organism

  17. Resources Pathway Tools http://bioinformatics.ai.sri.com/ptools MetaCychttp://www.metacyc.org

More Related