POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes

Lan, Yemin; Morrison, J. Calvin; Hershberg, Ruth; Rosen, Gail L.

doi:10.1093/nar/gkt1094

POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes

Journal Article · Tue Nov 05 00:00:00 EST 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkt1094· OSTI ID:1904534

Lan, Yemin ^[1]; Morrison, J. Calvin ^[2]; Hershberg, Ruth ^[3]; Rosen, Gail L. ^[2]

Drexel University, Philadelphia, PA (United States); Drexel Univ., Philadelphia, PA (United States)
Drexel University, Philadelphia, PA (United States)
Technion-Israel Institute of Technology, Haifa (Israel)

POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence identity across all orthologs shared by two genomes, (ii) genomic fluidity (a measure of gene content dissimilarity), (iii) number of ‘orthologs’ shared between two genomes, (iv) pairwise identity of the 16S ribosomal RNA genes and (v) pairwise identity of an additional 73 marker genes present in >90% prokaryotes. Users can visualize these metrics against each other in a 2D plot for exploratory analysis of genome similarity and of how different aspects of genome similarity relate to each other. The results of these comparisons are fully downloadable. In addition, users can download raw BLAST results for all or user-selected comparisons. Therefore, we provide users with full flexibility to carry out their own downstream analyses, by creating easy access to data that would normally require heavy computational resources to generate. POGO-DB should prove highly useful for researchers interested in comparative microbiology and benefit the microbiome/metagenomic communities by providing the information needed to select suitable phylogenetic marker genes within particular lineages.

View Accepted Manuscript (DOE)

Research Organization:: Drexel University, Philadelphia, PA (United States); Kent State University, Kent, OH (United States)

Sponsoring Organization:: Israeli Council for Higher Education; National Science Foundation (NSF); Robert J. Shillman Career Advancement Chair; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0004335

OSTI ID:: 1904534

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 42; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species Bolotin, Evgeni; Hershberg, Ruth Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01536	journal	August 2017

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