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Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Open accessAbstract
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.
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Metadata
- Authors
- Karp, P. D., Latendresse, M., Paley, S. M., Krummenacker, M., Ong, Q. D., Billington, R., Kothari, A., Weaver, D., Lee, T., Subhraveti, P., Spaulding, A., Fulcher, C., Keseler, I. M., & Caspi, R.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-10
- Volume
- 17
- Issue
- 5
- Pages
- 877-890
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W4236875018
- Cited by
- 266
- References
- 38
- FWCI
- 9.78
- Type
- journal article
- Language
- en
- Open access
- bronze
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