NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

Rogan Carr; Elhanan Borenstein

doi:10.1093/bioinformatics/btr721

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

Bioinformatics. 2012 Mar 1;28(5):734-5. doi: 10.1093/bioinformatics/btr721. Epub 2012 Jan 4.

Authors

Rogan Carr¹, Elhanan Borenstein

Affiliation

¹ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

PMID: 22219204
DOI: 10.1093/bioinformatics/btr721

Abstract

NetSeed is a web tool and Perl module for analyzing the topology of metabolic networks and calculating the set of exogenously acquired compounds. NetSeed is based on the seed detection algorithm, developed and validated in previous studies.

Availability: The NetSeed web-based tool, open-source Perl module, examples and documentation are freely available online at: http://depts.washington.edu/elbogs/NetSeed.

MeSH terms

Algorithms
Bacteria / metabolism*
Ecology
Environment
Internet
Metabolic Networks and Pathways*
Microbial Interactions
Software*