CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes

Svetlitsky, Dina, Dagan, Tal, Chalifa-Caspi, Vered, Ziv-Ukelson, Michal and Valencia, Alfonso (2018) CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes Bioinformatics . DOI 10.1093/bioinformatics/bty861.

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Supplementary data:

Abstract

Motivation:

Identification of conserved syntenic blocks across microbial genomes is important for several problems in comparative genomics such as gene annotation, study of genome organization and evolution, and prediction of gene interactions. Current tools for syntenic block discovery do not scale up to the large quantity of prokaryotic genomes available today.
Results:

We present a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. We present an efficient algorithm that identifies CSBs in large genomic datasets. The algorithm is implemented and incorporated in a novel tool with a graphical user interface, denoted CSBFinder, that ranks the discovered CSBs according to a probabilistic score and clusters them to families according to their gene content similarity. We apply CSBFinder to data mine 1,487 prokaryotic genomes including chromosomes and plasmids. For post-processing analysis, we generate heatmaps for visualizing the distribution of CSB family members across various taxa. We exemplify the utility of CSBFinder in operon prediction, in deciphering unknown gene function, and in taxonomic analysis of colinear syntenic blocks.

Document Type: Article
Research affiliation: Kiel University > Kiel Marine Science
OceanRep > The Future Ocean - Cluster of Excellence
Kiel University
Refereed: Yes
DOI etc.: 10.1093/bioinformatics/bty861
ISSN: 1367-4803
Projects: Future Ocean
Date Deposited: 16 Jan 2019 10:18
Last Modified: 17 Jan 2019 09:06
URI: http://eprints.uni-kiel.de/id/eprint/45372

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