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APPRIS 2017: principal isoforms for multiple gene sets.

Jose Manuel Rodriguez1, Juan Rodriguez-Rivas2, Tomás Di Domenico2

  • 1Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

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Summary
This summary is machine-generated.

The APPRIS database annotates protein splice isoforms using structural, functional, and conservation data. Updates include new species, expanded coverage, and reliability measures for principal isoforms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The Alternative Protein પરિવાર Isoform Annotation (APPRIS) database annotates splice isoforms in protein-coding genes.
  • It identifies a single 'principal' isoform as the reference for each gene, reflecting biological reality for most genes.
  • Principal APPRIS isoforms are the best predictors of main protein isoforms.

Purpose of the Study:

  • To present updates and new developments in the APPRIS database.
  • To expand APPRIS coverage to include new species and major gene sets.
  • To refine annotation methods and introduce reliability measures for principal isoforms.

Main Methods:

  • Annotation of splice isoforms using protein structural and functional features.
  • Cross-species conservation analysis to identify principal isoforms.
  • Integration of GENCODE/Ensembl, RefSeq, and UniProtKB gene sets for six organisms.

Main Results:

  • Addition of three new species: chimpanzee, Drosophila melanogaster, and Caenorhabditis elegans.
  • Expansion of APPRIS to cover RefSeq gene sets and UniProtKB proteomes for six species.
  • Refined annotation pipeline methods and the introduction of reliability scores for principal isoforms.

Conclusions:

  • The updated APPRIS database provides enhanced annotation of protein splice isoforms.
  • Expanded species coverage and refined methods improve the prediction of principal protein isoforms.
  • APPRIS serves as a valuable resource for understanding gene and protein diversity.