title: The MORPH-R web server and software tool for predicting missing genes in biological pathways.
abstract: A biological pathway is the set of molecular entities involved in a given biological process and the interrelations among them. Even though biological pathways have been studied extensively, discovering missing genes in pathways remains a fundamental challenge. Here, we present an easy-to-use tool that allows users to run MORPH (MOdule-guided Ranking of candidate PatHway genes), an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities. MORPH supports the analysis in tomato, Arabidopsis and the two new species: rice and the newly sequenced potato genome. The new tool, called MORPH-R, is available both as a web server (at http://bioinformatics.psb.ugent.be/webtools/morph/) and as standalone software that can be used locally. In the standalone version, the user can apply the tool to new organisms using any proprietary and public data sources.
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
authors.forename: David
authors.initials: D
authors.lastname: Amar
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
authors.forename: Itziar
authors.initials: I
authors.lastname: Frades
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent, Belgium.|Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.
authors.forename: Tim
authors.initials: T
authors.lastname: Diels
authors.affiliation: Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: David
authors.initials: D
authors.lastname: Zaltzman
authors.affiliation: Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Netanel
authors.initials: N
authors.lastname: Ghatan
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom.
authors.forename: Pete E
authors.initials: PE
authors.lastname: Hedley
authors.affiliation: Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Alexandersson
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent, Belgium.|Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Oren
authors.initials: O
authors.lastname: Tzfadia
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D053898:Biosynthetic Pathways / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics*; D020407:Internet; D018551:Solanum lycopersicum / Q000235:genetics; D012275:Oryza / Q000235:genetics; D015203:Reproducibility of Results; D012984:Software; D011198:Solanum tuberosum / Q000235:genetics