Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

By Marnix H. Medema, Eriko Takano, Rainer Breitling. Molecular biology and evolution, 2013

328 citations recorded by the source corpus.

The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user’s own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/ece19d91b496a342478151191ac85402ff6bac30

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Pharmacology

Citations in the corpus

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. (2014, methodology): “Bioinformatic Analysis of APE Gene Clusters Expansion of the APEBGC family was performed usingmanual parsing of MultiGeneBlast (Medema et al., 2013) architecture search results (with the E.”
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements (2018, methodology): “In addition, the ICEfinder has a comparison module (Supplementary Figure S5) that allows performing the alignment between the identified ICE loci against the ICEberg-archived ICEs using MultiGeneBlast (24).”
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers (2013, methodology): “In addition, an integrated version of MultiGene-Blast (21), ClusterBlast, is used to identify similar gene clusters in a comprehensive gene cluster database. antiSMASH 2.0 can be either installed locally on Windows, Mac OS X or Linux computers, or be accessed via the internet at…”
clinker & clustermap.js: Automatic generation of gene cluster comparison figures (2020, methodology): “Figures generated by clinker and clustermap.js are easily exported as scalable vector graphics (SVG) ﬁles that can be further modiﬁed in vector image software. clinker and clustermap.js can serve as a useful extension of gene cluster search tools such as MultiGeneBlast (Medema et al. , 2013) or cbla”