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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:BackgroundThe onset of the COVID-19 pandemic and the concurrent development of vaccines offered a rare and somewhat unprecedented opportunity to study antivaccination behavior as it formed over time via the use of archived versions of websites.ObjectiveThis study aims to assess how existing antivaccination websites modified their content to address COVID-19 vaccines and pandemic restrictions.MethodsUsing a preexisting collection of 25 antivaccination websites curated by the IvyPlus Web Collection Program prior to the pandemic and crawled every 6 months via Archive-It, we conducted a content analysis to see how these websites acknowledged or ignored COVID-19 vaccines and pandemic restrictions. Websites were assessed for financial behaviors such as having storefronts, mention of COVID-19 vaccines in general or by manufacturer name, references to personal freedom such as masking, safety concerns like side effects, and skepticism of science.ResultsThe majority of websites addressed COVID-19 vaccines in a negative fashion, with more websites making appeals to personal freedom or expressing skepticism of science than questioning safety. This can potentially be attributed to the lack of available safety data about the vaccines at the time of data collection. Many of the antivaccination websites we evaluated actively sought donations and had a membership option, evidencing these websites have financial motivations and actively build a community around these issues. The content analysis also offered the opportunity to test the viability of archived websites for use in scholarly research. The archived versions of the websites had significant shortcomings, particularly in search functionality, and required supplementation with the live websites. For web archiving to be a viable source of stand-alone content for research, the technology needs to make significant improvements in its capture abilities.ConclusionsIn summary, we found antivaccination websites existing prior to the COVID-19 pandemic largely adapted their messaging to address COVID-19 vaccines with very few sites ignoring the pandemic altogether. This study also demonstrated the timely and significant need for more robust web archiving capabilities as web-based environments become more ephemeral and unstable.

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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