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Development of ListeriaBase and comparative analysis of Listeria monocytogenes

Overview of attention for article published in BMC Genomics, October 2015
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Title
Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-1959-5
Pubmed ID
Authors

Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh VR Mutha, Wei Yee Wee, Hamed Heydari, Shi Yang Tan, Mia Yang Ang, Guat Jah Wong, Siew Woh Choo

Abstract

Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them. With this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes. ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my .

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 58 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 2%
Unknown 57 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 19%
Student > Master 9 16%
Student > Ph. D. Student 8 14%
Student > Bachelor 5 9%
Lecturer 5 9%
Other 12 21%
Unknown 8 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 15 26%
Biochemistry, Genetics and Molecular Biology 12 21%
Immunology and Microbiology 9 16%
Chemical Engineering 3 5%
Environmental Science 3 5%
Other 7 12%
Unknown 9 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 October 2015.
All research outputs
#20,293,238
of 22,829,683 outputs
Outputs from BMC Genomics
#9,281
of 10,655 outputs
Outputs of similar age
#233,234
of 277,991 outputs
Outputs of similar age from BMC Genomics
#340
of 360 outputs
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