Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast
Open Access
- 14 February 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in Molecular Biology and Evolution
- Vol. 30 (5), 1218-1223
- https://doi.org/10.1093/molbev/mst025
Abstract
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/.Keywords
This publication has 17 references indexed in Scilit:
- Ensembl 2012Nucleic Acids Research, 2011
- antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequencesNucleic Acids Research, 2011
- Prokaryotic gene clusters: A rich toolbox for synthetic biologyBiotechnology Journal, 2010
- BLAST+: architecture and applicationsBMC Bioinformatics, 2009
- Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management SystemPLOS ONE, 2009
- EDGAR: A software framework for the comparative analysis of prokaryotic genomesBMC Bioinformatics, 2009
- SynBlast: Assisting the analysis of conserved synteny informationBMC Bioinformatics, 2008
- PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomesBMC Bioinformatics, 2008
- The evolution of gene collectives: How natural selection drives chemical innovationProceedings of the National Academy of Sciences of the United States of America, 2008
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004