Protocols

POGO-DB specifications

Information


Unique identifier OMICS_17874
Name POGO-DB
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Ruth Hershberg

Publication for POGO-DB

POGO-DB citations

 (2)
call_split

Bacterial intra species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes

2016
Sci Rep
PMCID: 5062063
PMID: 27734920
DOI: 10.1038/srep35168
call_split See protocol

[…] es of strains belonging to the same bacterial species were compared in the pairwise manner using FASTA. Orthologous gene pairs were identified as reciprocal best hits. Following the thresholds set by POGO-DB, only putative orthologous gene pairs sharing 30% identity over at least 70% of the gene length were used for ANI calculation. Next, the % nucleotide identity of each pair of orthologs was cal […]

library_books

Databases for Microbiologists

2015
J Bacteriol
PMCID: 4505447
PMID: 26013493
DOI: 10.1128/JB.00330-15

[…] The Gene Ontology resource () was designed to unify the representation of genes and proteins across all species, and it is often used as a part of the genome annotation process. The main goal of the POGO-DB database () is to allow pairwise comparisons of microbial genomes and identification of orthologous genes. Identification of orthologs in bacterial and archaeal genomes is also the main scope […]

POGO-DB institution(s)
School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Electrical & Computer Engineering Department, Drexel University, Philadelphia, PA, USA; 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, Israel
POGO-DB funding source(s)
This work was supported by a National Science Foundation (NSF) CAREER award number [0845827], NSF award number [1120622], Department of Energy (DOE) Office of Science (BER) award [DE-SC0004335], ERC FP7 CIG grant [321780], by a Yigal Allon Fellowship awarded by the Israeli Council for Higher Education and by the Robert J. Shillman Career Advancement Chair.

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