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An Integrated Approach for Microprotein Identification and Sequence Analysis
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APPRIS: selecting functionally important isoforms.

Jose Manuel Rodriguez1, Fernando Pozo2, Daniel Cerdán-Vélez2

  • 1Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain.

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Summary
This summary is machine-generated.

The APPRIS database now includes annotations for 10 species, featuring new cow and chicken data. It integrates AlphaFold protein structures and TRIFID scores to identify principal protein isoforms.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • The APPRIS database annotates protein isoforms across species, identifying principal isoforms based on structure, function, and conservation.
  • Principal isoforms represent the main cellular protein product, supported by human genetic and proteomic data.
  • Previous APPRIS versions focused on core methods for principal isoform selection.

Purpose of the Study:

  • To report recent updates and expansions to the APPRIS database.
  • To enhance the accuracy and scope of protein isoform annotation.
  • To integrate new data sources and computational methods for isoform selection.

Main Methods:

  • Expanded APPRIS annotations to include cow and chicken.
  • Integrated protein structural models from the EMBL-EBI AlphaFold database.
  • Implemented TRIFID functional isoform scores for all splice isoforms.
  • Substantially increased human proteomic evidence for validation.

Main Results:

  • APPRIS now covers 10 model organisms with updated annotations.
  • New species (cow, chicken) and enhanced structural data (AlphaFold) are included.
  • TRIFID scores provide a novel method for functional isoform assessment.
  • Expanded proteomics data strengthens the validation of principal isoforms.

Conclusions:

  • The updated APPRIS database offers a more comprehensive resource for protein isoform information.
  • Integration of AlphaFold and TRIFID scores improves the identification of principal isoforms.
  • The expanded species coverage and data enhance APPRIS utility in comparative genomics and functional studies.