title: POGO-DB--a database of pairwise-comparisons of genomes and conserved orthologous genes.
abstract: 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.
authors.affiliation: School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA, Electrical & Computer Engineering Department, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA and Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
authors.forename: Yemin
authors.initials: Y
authors.lastname: Lan
authors.forename: J Calvin
authors.initials: JC
authors.lastname: Morrison
authors.forename: Ruth
authors.initials: R
authors.lastname: Hershberg
authors.forename: Gail L
authors.initials: GL
authors.lastname: Rosen
mesh_terms: D030541:Databases, Genetic; D064351:Genes, Microbial; D064349:Genome, Microbial; D023281:Genomics; D020407:Internet; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D020539:Sequence Analysis, Protein
chemical_list: D012336:RNA, Ribosomal, 16S