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Table 1 Major new features

From: Regulatory network operations in the Pathway Tools software

Ontology classes

Compound-Mediated-Translation-Regulation (riboswitches)

 

Allosteric-Regulation-of-RNAP

Visualizations

Regulation Summary Diagram (section The regulation summary diagram)

 

Specialized Signaling Pathway display and editing (section Pathway diagrams)

 

Port of Regulatory Overview (section Regulatory overview) to BioCyc website

Computational Analyses

Object Group Operations and Regulation Enrichment Analysis (section Object group operations and regulation-enrichment analysis) Export of Regulatory Network

 

to XGMML (Cytoscape) (section Export to cytoscape) Ranking Genes According

 

to Regulatory Influence (section Ranking genes according to regulatory influence)

 

Web services access to regulatory data

  1. Regulation-related features or capabilities described in this paper that are new in Pathway Tools since the last major Pathway Tools paper [1].
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BMC Bioinformatics

ISSN: 1471-2105

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