Dataset Information

MySyntenyPortal: an application package to construct websites for synteny block analysis.

ABSTRACT: BACKGROUND:Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. RESULTS:To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users' own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. CONCLUSIONS:mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user's own genome data.

SUBMITTER: Lee J

PROVIDER: S-EPMC5989462 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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mySyntenyPortal: an application package to construct websites for synteny block analysis.

Lee Jongin J Lee Daehwan D Sim Mikang M Kwon Daehong D Kim Juyeon J Ko Younhee Y Kim Jaebum J

BMC bioinformatics 20180605 1

<h4>Background</h4>Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces c ...[more]

PMID: 29871588

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Project description:BackgroundOwing to the fact that firefighters have unique health risks, access to firefighter-specific internet-based health information is a potential mechanism for achieving better health and work outcomes.ObjectiveThe objective of our study was to identify the amount and nature of health information resources available on Canadian firefighter-specific websites and the extent to which resources are consistent across websites as a surrogate indicator of diffusion of information.MethodsA search of health resources on firefighter websites (union and employer) for all Canadian provinces, major cities and a subset of smaller cities, and the International Association of Fire Fighters (IAFF) website was conducted on Google (July 2017). Content was identified and classified based on the type of resource, health focus, and location. The quantity and nature of the resources were summarized using descriptive statistics.ResultsAmong all (N=313) websites reviewed, 41 websites had health information with a cumulative total of 128 resources that addressed firefighter mental (59/128, 46.1%), physical (43/128, 33.6%), and work health (26/128, 20.3%). The highest density of information was found on international and national websites (13 resources per website) and the least on local websites (1 resource per 7 websites). Three provinces (Ontario, Québec, and British Columbia) hosted 81% (65/80) of the provincial, territorial and local resources. General mental health (20/59, 34%), posttraumatic stress disorder (14/59, 24%), and suicide (14/59, 24%) were the most prevalent topics within the mental health resources, whereas half (21/43, 49%) of all physical health resources were on cancer. No resources from Northern Canada were found. Musculoskeletal health was not mentioned in any of the resources identified. There was minimal cross-linking of resources across sites (only 4 resources were duplicated across sites), and there was no clear indication of how the content was vetted or evaluated for quality.ConclusionsThere was wide variation in the amount and type of information available on different firefighter websites with limited diffusion of information across jurisdictions. Quality evaluation and coordination of resources should be considered to enhance firefighters' access to quality health information to meet their specific needs. Mental health and cancer information aligned with high rates of these health problems in firefighters, whereas the lack of information on musculoskeletal health was discordant with their high rate of work injury claims for these problems.

Dataset Information

MySyntenyPortal: an application package to construct websites for synteny block analysis.

Publications

mySyntenyPortal: an application package to construct websites for synteny block analysis.

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