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Protocols

CoreGenes specifications

Information


Unique identifier OMICS_17814
Name CoreGenes
Interface Web user interface
Restrictions to use None
Input data NCBI-GenBank accession numbers.
Output data A graphical output and/or tabular display.
Programming languages Java
Computer skills Basic
Version 1.0
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for CoreGenes

CoreGenes citations

 (61)
library_books

Two New Lytic Bacteriophages of the Myoviridae Family Against Carbapenem Resistant Acinetobacter baumannii

2018
Front Microbiol
PMCID: 5936750
PMID: 29760690
DOI: 10.3389/fmicb.2018.00850

[…] omy_updates_since_the_8th_report/m/prokaryote-official/5901) (Adams et al., ) was taken as the reference to determine the taxonomy of the bacteriophages. Mauve (http://asap.ahabs.wisc.edu/mauve/) and CoreGenes (Zafar et al., ; Mahadevan et al., ,) were used to compare the genomic organization and core genes for a given group of bacteriophages. Phylogenetic tree for taxonomic analysis was construct […]

library_books

Elucidation of the anti hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

2018
BMC Genomics
PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] hage regions within the genome were identified using PHAST. Whole-genome nucleotide alignments were generated and visualized by Mauve. Identification of core genes and unique genes was carried out by coregenes 3.0. […]

library_books

Comparative Analysis of 37 Acinetobacter Bacteriophages

2017
Viruses
PMCID: 5795418
PMID: 29295549
DOI: 10.3390/v10010005

[…] e proteins and between 68 and 89 proteins that form accessory protein groups. Gene products unique to each phage occupy approximately 20% of the genome. Relative to other members of the Tevenvirinae, CoreGenes analysis indicates that >40% of the gene products have a homolog encoded by T4, RB69, RB49, JS98, SP18, JD18 and CC31 ().The presence of homologs to Alt, MotA, AsiA and gp55 in the Cluster A […]

library_books

Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano

2017
Nat Commun
PMCID: 5730564
PMID: 29242515
DOI: 10.1038/s41467-017-02214-8

[…] emove alternative transcripts with identical CDS, and to exclude non-coding transcripts and transcripts overlapping repeat annotations. This final transcriptome assembly was named Mlig_RNA_3_7_DV1.v1.coregenes and used in annotation of the Mlig_3_7 genome assembly for submission to DDBJ/ENA/GenBank. […]

library_books

The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages

2017
Sci Rep
PMCID: 5648845
PMID: 29051555
DOI: 10.1038/s41598-017-13911-1

[…] arx and CcrRogue (results not shown), showing both that BLASTN is not sensitive enough to detect such low nucleotide similarity and that the genomes are indeed distantly related. This is supported by CoreGenes (results not shown) and by the maximum likelihood trees on major capsid protein and DNA polymerase (Supplementary Fig. ), showing that Lacusarx and DSS3Φ8 are each as distantly related to th […]

call_split

Identification and genomic comparison of temperate bacteriophages derived from emetic Bacillus cereus

2017
PLoS One
PMCID: 5590980
PMID: 28886124
DOI: 10.1371/journal.pone.0184572
call_split See protocol

[…] is of the phages at the nucleotide level was conducted using Gegenees 2.1 (window size of 50 bp, step-size of 25 bp, and cutoff of 30%) and Mauve, and comparison at the proteomic level was made using CoreGenes 3.0 (http://binf.gmu.edu:8080/CoreGenes3.0). Genes with scores above 75 were regarded as core genes [, , ]. The protein sequences of the tail fibers used for alignment were available from th […]

Citations

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CoreGenes institution(s)
School of Computational Sciences, George Mason University, Manassas, VA, USA; Center for Biomedical Genomics and Informatics, College of Arts and Sciences, George Mason University, Manassas, VA, USA
CoreGenes funding source(s)
Funded in part by a grant from the American Type Culture Collection and also by a Faculty Development Award from the Office of the Provost (GMU).

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