Displaying publications 1 - 20 of 26 in total

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  1. Fulltext VibrioBase: a model for next-generation genome and annotation database development
    Choo SW, Heydari H, Tan TK, Siow CC, Beh CY, Wee WY, et al.
    ScientificWorldJournal, 2014;2014:569324.
    PMID: 25243218 DOI: 10.1155/2014/569324
    To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community. VibrioBase currently houses a total of 252 Vibrio genomes developed in a user-friendly manner and useful to enable the analysis of these genomic data, particularly in the field of comparative genomics. Besides general data browsing features, VibrioBase offers analysis tools such as BLAST interfaces and JBrowse genome browser. Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. Both of these tools will enable researchers with little experience in bioinformatics to get meaningful information from Vibrio genomes with ease. We have tested the validity and suitability of these tools and features for use in the next-generation database development.
  2. A collective statement in support of saving pangolins
    Choo SW, Chong JL, Gaubert P, Hughes AC, O'Brien S, Chaber AL, et al.
    Sci Total Environ, 2022 Feb 14.
    PMID: 35176378 DOI: 10.1016/j.scitotenv.2022.153666
  3. Rapid assessment of total MCPD esters in palm-based cooking oil using ATR-FTIR application and chemometric analysis
    Goh KM, Maulidiani M, Rudiyanto R, Wong YH, Ang MY, Yew WM, et al.
    Talanta, 2019 Jun 01;198:215-223.
    PMID: 30876552 DOI: 10.1016/j.talanta.2019.01.111
    The technique of Fourier transform infrared spectroscopy is widely used to generate spectral data for use in the detection of food contaminants. Monochloropropanediol (MCPD) is a refining process-induced contaminant that is found in palm-based fats and oils. In this study, a chemometric approach was used to evaluate the relationship between the FTIR spectra and the total MCPD content of a palm-based cooking oil. A total of 156 samples were used to develop partial least squares regression (PLSR), artificial neural network (nnet), average artificial neural network (avNNET), random forest (RF) and cubist models. In addition, a consensus approach was used to generate fusion result consisted from all the model mentioned above. All the models were evaluated based on validation performed using training and testing datasets. In addition, the box plot of coefficient of determination (R2), root mean square error (RMSE), slopes and intercepts by 100 times randomization was also compared. Evaluation of performance based on the testing R2 and RMSE suggested that the cubist model predicted total MCPD content with the highest accuracy, followed by the RF, avNNET, nnet and PLSR models. The overfitting tendency was assessed based on differences in R2 and RMSE in the training and testing calibrations. The observations showed that the cubist and avNNET models possessed a certain degree of overfitting. However, the accuracy of these models in predicting the total MCPD content was high. Results of the consensus model showed that it slightly improved the accuracy of prediction as well as significantly reduced its uncertainty. The important variables derived from the cubist and RF models suggested that the wavenumbers corresponding to the MCPDs originated from the -CH=CH2 or CH=CH (990-900 cm-1) and C-Cl stretch (800-700 cm-1) regions of the FTIR spectrum data. In short, chemometrics in combination with FTIR analysis especially for the consensus model represent a potential and flexible technique for estimating the total MCPD content of refined vegetable oils.
  4. Fulltext MycoCAP - Mycobacterium Comparative Analysis Platform
    Choo SW, Ang MY, Dutta A, Tan SY, Siow CC, Heydari H, et al.
    Sci Rep, 2015 Dec 15;5:18227.
    PMID: 26666970 DOI: 10.1038/srep18227
    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my.
  5. Fulltext Parvimonas micra, Peptostreptococcus stomatis, Fusobacterium nucleatum and Akkermansia muciniphila as a four-bacteria biomarker panel of colorectal cancer
    Osman MA, Neoh HM, Ab Mutalib NS, Chin SF, Mazlan L, Raja Ali RA, et al.
    Sci Rep, 2021 02 03;11(1):2925.
    PMID: 33536501 DOI: 10.1038/s41598-021-82465-0
    Dysbiosis of the gut microbiome has been associated with the pathogenesis of colorectal cancer (CRC). We profiled the microbiome of gut mucosal tissues from 18 CRC patients and 18 non-CRC controls of the UKM Medical Centre (UKMMC), Kuala Lumpur, Malaysia. The results were then validated using a species-specific quantitative PCR in 40 CRC and 20 non-CRC tissues samples from the UMBI-UKMMC Biobank. Parvimonas micra, Fusobacterium nucleatum, Peptostreptococcus stomatis and Akkermansia muciniphila were found to be over-represented in our CRC patients compared to non-CRC controls. These four bacteria markers distinguished CRC from controls (AUROC = 0.925) in our validation cohort. We identified bacteria species significantly associated (cut-off value of > 5 fold abundance) with various CRC demographics such as ethnicity, gender and CRC staging; however, due to small sample size of the discovery cohort, these results could not be further verified in our validation cohort. In summary, Parvimonas micra, Fusobacterium nucleatum, Peptostreptococcus stomatis and Akkermansia muciniphila were enriched in our local CRC patients. Nevertheless, the roles of these bacteria in CRC initiation and progression remains to be investigated.
  6. Connecting Proteomics to Next-Generation Sequencing: Proteogenomics and Its Current Applications in Biology
    Low TY, Mohtar MA, Ang MY, Jamal R
    Proteomics, 2019 05;19(10):e1800235.
    PMID: 30431238 DOI: 10.1002/pmic.201800235
    Understanding the relationship between genotypes and phenotypes is essential to disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes and proteins are closely linked in biological systems. However, genomics and proteomics have developed separately into two distinct disciplines whereby crosstalk among scientists from the two domains is limited and this constrains the integration of both fields into a single data modality of useful information. The emerging field of proteogenomics attempts to address this by building bridges between the two disciplines. In this review, how genomics and transcriptomics data in different formats can be utilized to assist proteogenomics application is briefly discussed. Subsequently, a much larger part of this review focuses on proteogenomics research articles that are published in the last five years that answer two important questions. First, how proteogenomics can be applied to tackle biological problems is discussed, covering genome annotation and precision medicine. Second, the latest developments in analytical technologies for data acquisition and the bioinformatics tools to interpret and visualize proteogenomics data are covered.
  7. Fulltext CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips
    Heydari H, Siow CC, Tan MF, Jakubovics NS, Wee WY, Mutha NV, et al.
    PLoS One, 2014;9(1):e86318.
    PMID: 24466021 DOI: 10.1371/journal.pone.0086318
    Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.
  8. Fulltext Comparative Genomic Analysis Reveals a Possible Novel Non-Tuberculous Mycobacterium Species with High Pathogenic Potential
    Choo SW, Dutta A, Wong GJ, Wee WY, Ang MY, Siow CC
    PLoS One, 2016;11(4):e0150413.
    PMID: 27035710 DOI: 10.1371/journal.pone.0150413
    Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis. Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular phylogenetic, comparative genomic, ANI and AAI analyses. UM_CSW is closely related to the Mycobacterium avium complex. While it has characteristic features of an environmental bacterium, it also shows a high pathogenic potential with the presence of a wide variety of putative genes related to bacterial virulence and shares very similar pathogenomic profiles with the known pathogenic mycobacterial species. Thus, we conclude that this possible novel Mycobacterium species should be tightly monitored for its possible causative role in human infections.
  9. 1 H-NMR metabolomics for evaluating the protective effect of Clinacanthus nutans (Burm. f) Lindau water extract against nitric oxide production in LPS-IFN-γ activated RAW 264.7 macrophages
    Khoo LW, Kow ASF, Maulidiani M, Ang MY, Chew WY, Lee MT, et al.
    Phytochem Anal, 2019 Jan;30(1):46-61.
    PMID: 30183131 DOI: 10.1002/pca.2789
    INTRODUCTION: Clinacanthus nutans, a small shrub that is native to Southeast Asia, is commonly used in traditional herbal medicine and as a food source. Its anti-inflammation properties is influenced by the metabolites composition, which can be determined by different binary extraction solvent ratio and extraction methods used during plant post-harvesting stage.

    OBJECTIVE: Evaluate the relationship between the chemical composition of C. nutans and its anti-inflammatory properties using nuclear magnetic resonance (NMR) metabolomics approach.

    METHODOLOGY: The anti-inflammatory effect of C. nutans air-dried leaves extracted using five different binary extraction solvent ratio and two extraction methods was determined based on their nitric oxide (NO) inhibition effect in lipopolysaccharide-interferon-gamma (LPS-IFN-γ) activated RAW 264.7 macrophages. The relationship between extract bioactivity and metabolite profiles and quantifications were established using 1 H-NMR metabolomics and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The possible metabolite biosynthesis pathway was constructed to further strengthen the findings.

    RESULTS: Water and sonication prepared air-dried leaves possessed the highest NO inhibition activity (IC50  = 190.43 ± 12.26 μg/mL, P 

  10. Fulltext NeisseriaBase: a specialised Neisseria genomic resource and analysis platform
    Zheng W, Mutha NV, Heydari H, Dutta A, Siow CC, Jakubovics NS, et al.
    PeerJ, 2016;4:e1698.
    PMID: 27017950 DOI: 10.7717/peerj.1698
    Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.
  11. Fulltext Draft Genome Sequences of Four Methicillin-Resistant Staphylococcus aureus Strains (M080_2017, M106_2017, M181_2017, and M191_2017), Isolated from a Malaysian Teaching Hospital
    Ang MY, Binti Mohamad Farook NA, Kamarudin N, Lam SD, Di Gregorio S, Tengku Jamaluddin TZM, et al.
    Microbiol Resour Announc, 2022 Dec 15;11(12):e0086722.
    PMID: 36413024 DOI: 10.1128/mra.00867-22
    Draft genome sequences were obtained for four methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from various wards of the Hospital Canselor Tuanku Muhriz (HCTM), Kuala Lumpur, Malaysia, in 2017. Using different bioinformatics tools, we annotated the draft genomes and identified multiple antimicrobial resistance genes.
  12. Fulltext Optimization of Residual Hexane in Edible Oils Analysis Using Static Headspace Gas Chromatography
    Samsuri AH, Ang MY, Ng SY
    Int J Anal Chem, 2021;2021:1941336.
    PMID: 34745265 DOI: 10.1155/2021/1941336
    This study aims to determine the residual hexane in four edible oils in Malaysia using a simple, rapid, and automated method in order to improve the efficiency and productivity of the analysis. Gas chromatography (GC/FID) equipped with a headspace autosampler (HS-20) was used to perform the analysis. Incubation time for each injection was successfully optimized from one hour to 30 minutes (50% reduction) compared to the official AOCS method Ca 3b-87. Out of the four tested edible oils, only the hexane residues detected in sunflower oil exceeded the maximum residue limit (MRL) set by the European Union regulation. Significant difference of the results obtained between large calibration range (0-938 mg kg-1) and small calibration range (0-68 mg kg-1) suggests that there is a need to use a lower standard calibration concentration to avoid misinterpretation of analysis results. Method validation applies to the technical hexane; 2-methylpentane, 3-methylpentane, cyclohexane, and methylcyclopentane, the signal-to-noise (S/N), as well as the limit of quantification (LoQ) values was found to be 218.20, 221.45, 746.37, 97.37 and 0.85, 0.84, 0.25, 1.93 mg kg-1, respectively. Good linearity, repeatability, and low carryover of this method have provided an alternative way to analyze the content of the residual hexane in edible oils in a more efficient manner. Current study might provide a fundamental reference for the improvement of the AOCS official Ca 3b-87 method for determination of hexane residues in fats and oils analysis in the future.
  13. Comparative Genome Analysis of Fusobacterium nucleatum
    Ang MY, Dutta A, Wee WY, Dymock D, Paterson IC, Choo SW
    Genome Biol Evol, 2016 10 05;8(9):2928-2938.
    PMID: 27540086
    Fusobacterium nucleatum is considered to be a key oral bacterium in recruiting periodontal pathogens into subgingival dental plaque. Currently F. nucleatum can be subdivided into five subspecies. Our previous genome analysis of F. nucleatum W1481 (referred to hereafter as W1481), isolated from an 8-mm periodontal pocket in a patient with chronic periodontitis, suggested the possibility of a new subspecies. To further investigate the biology and relationships of this possible subspecies with other known subspecies, we performed comparative analysis between W1481 and 35 genome sequences represented by the five known Fusobacterium subspecies. Our analyses suggest that W1481 is most likely a new F. nucleatum subspecies, supported by evidence from phylogenetic analyses and maximal unique match indices (MUMi). Interestingly, we found a horizontally transferred W1481-specific genomic island harboring the tripartite ATP-independent (TRAP)-like transporter genes, suggesting this bacterium might have a high-affinity transport system for the C4-dicarboxylates malate, succinate, and fumarate. Moreover, we found virulence genes in the W1481 genome that may provide a strong defense mechanism which might enable it to colonize and survive within the host by evading immune surveillance. This comparative study provides better understanding of F. nucleatum and the basis for future functional work on this important pathogen.
  14. Fulltext Genome Sequence of Parvimonas micra Strain A293, Isolated from an Abdominal Abscess from a Patient in the United Kingdom
    Ang MY, Dymock D, Tan JL, Thong MH, Tan QK, Wong GJ, et al.
    Genome Announc, 2013;1(6).
    PMID: 24309744 DOI: 10.1128/genomeA.01025-13
    Parvimonas micra is an important oral microbe that has the ability to grow and proliferate within oral biofilms and is involved in periodontal disease, leading to gingival bleeding, gingival recession, alveolar bone loss, and tooth mobility. However, occasionally these normally oral pathogens can cause infections at other sites in the body. We present the genome sequence of Parvimonas micra strain A293, a smooth Parvimonas micra strain isolated from an abdominal abscess from a patient at Barts Hospital, London, United Kingdom.
  15. Fulltext Genome Sequence of Fusobacterium nucleatum Strain W1481, a Possible New Subspecies Isolated from a Periodontal Pocket
    Ang MY, Dymock D, Tan JL, Thong MH, Tan QK, Wong GJ, et al.
    Genome Announc, 2014;2(1).
    PMID: 24526626 DOI: 10.1128/genomeA.00009-14
    Fusobacterium nucleatum is a bacterial species commonly detected in dental plaque within the human oral cavity, with some strains associated with periodontal disease, one of the most common clinical bacterial infections in the human body. The exact mechanisms of its pathogenesis are still not completely understood. In this study, we present the genome sequence and annotation of F. nucleatum strain W1481, isolated from a periodontal pocket of a dental patient at the University of Bristol, United Kingdom, the 16S rRNA gene sequencing of which showed it to be markedly different from the five previously named subspecies.
  16. Fulltext First Whole-Genome Sequence of Mycobacterium iranicum, a Newly Reported Mycobacterial Species
    Tan JL, Ng HF, Wee WY, Ang MY, Wong GJ, Ngeow YF, et al.
    Genome Announc, 2013;1(5).
    PMID: 24072861 DOI: 10.1128/genomeA.00732-13
    Mycobacterium iranicum is a new species of nontuberculous mycobacterium reported in 2013. Here, we describe the first whole-genome sequence of this species, that of M. iranicum strain UM_TJL, isolated from a patient in Malaysia.
  17. Comparison assessment between SIM and MRM mode in the analysis of 3-MCPD ester, 2-MCPD ester and glycidyl ester
    Goh KM, Wong YH, Ang MY, Yeo SCM, Abas F, Lai OM, et al.
    Food Res Int, 2019 07;121:553-560.
    PMID: 31108780 DOI: 10.1016/j.foodres.2018.12.013
    The detection of 3- and 2-MCPD ester and glycidyl ester was transformed from selected ion monitoring (SIM) mode to multiple reaction monitoring (MRM) mode by gas chromatography triple quadrupole spectrometry. The derivatization process was adapted from AOCS method Cd 29a-13. The results showed that the coefficient of determination (R2) of all detected compounds obtained from both detection mode was comparable, which falls between 0.997 and 0.999. The limit of detection and quantification (LOD and LOQ) were improved in MRM mode as compared to SIM mode. In MRM mode, the LOD of 3- and 2-MCPD ester was achieved 0.01 mg/kg while the LOQ was 0.05 mg/kg. Besides, LOD and LOQ of glycidyl ester were 0.024 and 0.06 mg/kg respectively. A blank spiked with MCPD esters (0.03, 0.10 and 0.50 mg/kg) and GE (0.06, 0.24 and 1.20 mg/kg) were chosen for repeatability and recovery tests. MRM mode showed better repeatability in area ratio and recovery with relative standard deviation (RSD %) 
  18. Occurrence and risk assessment of 3-monochloropropanediols esters (3-MCPDE), 2-monochloropropanediol esters (2-MCPDE), and glycidyl esters (GE) in commercial infant formula samples from Malaysia
    Nik Azmi NNA, Tan TC, Ang MY, Leong YH
    Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2023 Feb;40(2):212-221.
    PMID: 36602442 DOI: 10.1080/19440049.2022.2163054
    The presence of 3-monochloropropanediol esters (3-MCPDE), 2-monochloropropanediol esters (2-MCPDE) and glycidyl esters (GE) in infant formula products has raised serious concerns. They incorporate vegetable oils, particularly palm-based oils, which are well-known to contain large amounts of these process contaminants. An analysis was conducted on infant formula samples (n = 16) obtained from the Malaysian market to determine the levels of 3-MCPDE, 2-MCPDE and GE using gas chromatography-mass spectrometry (GC-MS). The method was validated, with a limit of quantification (LOQ) on instrument of 0.10 µg/g for all analytes. The median concentrations of 3-MCPDE, 2-MCPDE and GE in infant formula in this study were 0.008 µg/g, 0.003 µg/g and 0.002 µg/g respectively. The estimated dietary intakes calculated from consumption of infant formula show higher exposures to infants within the age group of 0 to 5 months, highest for GE (1.61 µg/kg bw/day), followed by 3-MCPDE (0.68 µg/kg bw/day) and 2-MCPDE (0.41 µg/kg bw/day) compared to the age group of 6 to 12 months. Only one sample, relating to GE exposure is a potential risk for both age groups with MOE value below 25,000.
  19. Fulltext FusoBase: an online Fusobacterium comparative genomic analysis platform
    Ang MY, Heydari H, Jakubovics NS, Mahmud MI, Dutta A, Wee WY, et al.
    Database (Oxford), 2014;2014.
    PMID: 25149689 DOI: 10.1093/database/bau082
    Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram.
  20. Fulltext StaphyloBase: a specialized genomic resource for the staphylococcal research community
    Heydari H, Mutha NV, Mahmud MI, Siow CC, Wee WY, Wong GJ, et al.
    Database (Oxford), 2014;2014:bau010.
    PMID: 24578355 DOI: 10.1093/database/bau010
    With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/.
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