title: Development of ListeriaBase and comparative analysis of Listeria monocytogenes.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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 .
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. muifern007@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. muifern007@gmail.com.
authors.forename: Mui Fern
authors.initials: MF
authors.lastname: Tan
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. cheukchuen@gmail.com.
authors.forename: Cheuk Chuen
authors.initials: CC
authors.lastname: Siow
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. avirupdutta@gmail.com.
authors.forename: Avirup
authors.initials: A
authors.lastname: Dutta
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. nareshmvr@gmail.com.
authors.forename: Naresh Vr
authors.initials: NV
authors.lastname: Mutha
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. gavinwwy89@hotmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. gavinwwy89@hotmail.com.
authors.forename: Wei Yee
authors.initials: WY
authors.lastname: Wee
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. heydarihamed@yahoo.com.|Computer Science and Engineering Department, University of Nebraska-Lincoln, Lincoln, NE, 1468588-0115, USA. heydarihamed@yahoo.com.
authors.forename: Hamed
authors.initials: H
authors.lastname: Heydari
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. shiyangtan@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. shiyangtan@gmail.com.
authors.forename: Shi Yang
authors.initials: SY
authors.lastname: Tan
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. angmiayang@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. angmiayang@gmail.com.
authors.forename: Mia Yang
authors.initials: MY
authors.lastname: Ang
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. winnie.my23dna@gmail.com.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. winnie.my23dna@gmail.com.
authors.forename: Guat Jah
authors.initials: GJ
authors.lastname: Wong
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. lchoo@um.edu.my.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. lchoo@um.edu.my.|Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, Kuala Lumpur, 50603, Malaysia. lchoo@um.edu.my.
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
mesh_terms: D002874:Chromosome Mapping; D019143:Evolution, Molecular; D005819:Genetic Markers; D016680:Genome, Bacterial; D006801:Humans; D008089:Listeria monocytogenes / Q000235:genetics* / Q000472:pathogenicity; D008088:Listeriosis / Q000235:genetics* / Q000382:microbiology; D010802:Phylogeny
chemical_list: D005819:Genetic Markers