Michael Banf1,2, Kangmei Zhao1, Seung Y Rhee1. 1. Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA. 2. EducatedGuess.ai, Siegen, Germany.
Abstract
SUMMARY: Plants and microbes produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have yet to be elucidated. Some biosynthetic pathways are encoded by enzymes collocated in the chromosome. To facilitate a more comprehensive condition and tissue-specific expression analysis of metabolic gene clusters, we developed METACLUSTER, a probabilistic framework for characterizing metabolic gene clusters using context-specific gene expression information. AVAILABILITY AND IMPLEMENTATION: METACLUSTER is freely available at https://github.com/mbanf/METACLUSTER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Plants and microbes produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have yet to be elucidated. Some biosynthetic pathways are encoded by enzymes collocated in the chromosome. To facilitate a more comprehensive condition and tissue-specific expression analysis of metabolic gene clusters, we developed METACLUSTER, a probabilistic framework for characterizing metabolic gene clusters using context-specific gene expression information. AVAILABILITY AND IMPLEMENTATION: METACLUSTER is freely available at https://github.com/mbanf/METACLUSTER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Ben Field; Anna-Sophie Fiston-Lavier; Ariane Kemen; Katrin Geisler; Hadi Quesneville; Anne E Osbourn Journal: Proc Natl Acad Sci U S A Date: 2011-08-29 Impact factor: 11.205
Authors: Afrodite Krokida; Costas Delis; Katrin Geisler; Constantine Garagounis; Daniela Tsikou; Luis M Peña-Rodríguez; Dimitra Katsarou; Ben Field; Anne E Osbourn; Kalliope K Papadopoulou Journal: New Phytol Date: 2013-07-26 Impact factor: 10.151
Authors: Daniel Morgan; Matthew Studham; Andreas Tjärnberg; Holger Weishaupt; Fredrik J Swartling; Torbjörn E M Nordling; Erik L L Sonnhammer Journal: Sci Rep Date: 2020-08-25 Impact factor: 4.379