solcyc.solgenomics.net solcyc.solgenomics.net

solcyc.solgenomics.net

My Pathway Tools Web Site Home Page

A collection of model organism databases of metabolic pathways, including reactions, enzymes, genes and substrate compounds

http://solcyc.solgenomics.net/

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My Pathway Tools Web Site Home Page | solcyc.solgenomics.net Reviews
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A collection of model organism databases of metabolic pathways, including reactions, enzymes, genes and substrate compounds
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1 metabolism
2 pathways
3 metabolic
4 enzymes
5 compounds
6 reactions
7 biochemical
8 bioinformatics
9 model organism database
10 genes
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hide,show operations,operations,solcyc server,searching,change organism database,search compounds,search reactions,search pathways,search growth media,advanced search,blast search,genome,genome browser,genome overview,regulatory overview,metabolism,news
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My Pathway Tools Web Site Home Page | solcyc.solgenomics.net Reviews

https://solcyc.solgenomics.net

A collection of model organism databases of metabolic pathways, including reactions, enzymes, genes and substrate compounds

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solcyc.solgenomics.net solcyc.solgenomics.net
1

Regulatory Overview

http://solcyc.solgenomics.net/overviewsWeb/regOv.shtml

Search Genes, Proteins or RNAs. Google Search of this Site. Browse Enzyme Commission Ontology. Pan left/right/up/down the entire diagram by holding the left mouse button, left-click on gene node to open its gene page, right-click (ctrl-click for Mac) on gene or blank area for menus. Highlighting by Gene Name Substring. Include Regulatory Arrows Between Genes Found. Highlighting by Gene Name or Frame Id. Highlighting by Gene Ontology Terms. Include Regulatory Arrows Between Genes Found.

2

Dead-End Metabolite Finder

http://solcyc.solgenomics.net/dead-end-form.shtml

Search Genes, Proteins or RNAs. Google Search of this Site. Browse Enzyme Commission Ontology. DEMs) are metabolites that are either only consumed, or only produced, by the reactions within a given cellular compartment, including transport reactions. Although some DEMs are biologically accurate, many DEMs aid in identifying incomplete or incorrect curation of a PGDB. Include all molecules as potential DEMs. Limit DEM search to small molecules. Include non-pathway reactions in search.

3

Pathway/Genome Database Concepts Guide

http://solcyc.solgenomics.net/PGDBConceptsGuide.shtml

Search Genes, Proteins or RNAs. Google Search of this Site. Browse Enzyme Commission Ontology. Pathway/Genome Database Concepts Guide. 2 What Mechanisms Exist for Accessing PGDB Data? 43 Reaction Locations and Compartments of Metabolites. 44 Reaction Balancing and Protonation State in PGDBs. 441 Background and Motivations. 442 Protonation State Normalization. 443 Computational Reaction Balancing for Hydrogen. 444 Statistics on Reaction Balance and Protonation. 45 Reaction Atom Mappings. PGDBs can be load...

4

Comparative Analysis and Statistics

http://solcyc.solgenomics.net/comp-genomics

Search Genes, Proteins or RNAs. Google Search of this Site. Browse Enzyme Commission Ontology. Comparative Analysis and Statistics. This page allows you to compute statistics for a single Pathway/Genome Database, and to compute comparisons across multiple Pathway/Genome Databases for the set of organisms listed below. Note that computing summary statistics for the organism databases you have chosen may take several minutes. For faster operation, install Pathway Tools on your own computer! Transcription U...

5

Glossary

http://solcyc.solgenomics.net/glossary.shtml

Search Genes, Proteins or RNAs. Google Search of this Site. Browse Enzyme Commission Ontology. 0-Centered Scale, Omics Viewer. 0-centered scale: implies that the numerical data of the Omics Viewer data file can contain positive and negative values. The value 0 is considered to be the center of the numerical values provided in the data file. 1-Centered Scale, Omics Viewer. A term that identifies one end of a single-stranded nucleic acid. To the right, in reference to the direction of DNA. From the 3' end.

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pcp.oxfordjournals.org pcp.oxfordjournals.org

CathaCyc, a Metabolic Pathway Database Built from Catharanthus roseus RNA-Seq Data

http://pcp.oxfordjournals.org/content/54/5/673.long

Plant and Cell Physiology. View Current Issue (Volume 57 Issue 8 August 2016). Plant and Cell Physiology. CathaCyc, a Metabolic Pathway Database Built from. Gino J.E. Baart. Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium. Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium. Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000 Gent, Belgium. These authors contributed equally to this work. December 14, 2012.

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