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Related Concept Videos

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A schema is a mental construct consisting of a cluster or collection of related concepts (Bartlett, 1932). There are many different types of schemata, and they all have one thing in common: schemata are a method of organizing information that allows the brain to work more efficiently. When a schema is activated, the brain makes immediate assumptions about the person or object being observed.
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HMMER web server: 2018 update.

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Summary
This summary is machine-generated.

The HMMER webserver now offers expanded database searches and enhanced data integration. Users can access results via API for third-party use and explore biological context with new cross-references.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The HMMER webserver provides sequence similarity searches using profile hidden Markov models (HMMs).
  • Existing functionalities allowed result summarization and filtering by domain architecture or taxonomy.
  • There was a need for expanded data access and integration capabilities for large-scale use.

Purpose of the Study:

  • To enhance the HMMER webserver's utility for researchers.
  • To improve data accessibility and integration for large-scale bioinformatics analyses.
  • To provide richer biological context for search results.

Main Methods:

  • Expanded the HMMER webserver's application programmatic interface (API) to include all result presentations.
  • Refactored the JavaScript visualization library into standalone components consumable via the API.
  • Increased the number of searchable sequence datasets to 12 and profile HMM libraries to 6.
  • Integrated cross-references to other EMBL-EBI databases within search results.

Main Results:

  • All HMMER webserver result presentations are now available via both HTML and API.
  • Standalone visualization components can be integrated into third-party websites.
  • The webserver now searches against an expanded range of 12 sequence datasets and 6 profile HMM libraries.
  • Search results are enriched with cross-references to other EMBL-EBI resources.

Conclusions:

  • The enhanced HMMER webserver offers greater flexibility and data integration for bioinformatics research.
  • Expanded API access and standalone visualization components facilitate third-party application development.
  • Improved data discovery through expanded databases and cross-references aids biological context exploration.