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Nucleic Acids Res. 2018 Jan 4;46(D1):D213-D217. doi: 10.1093/nar/gkx997.

APPRIS 2017: principal isoforms for multiple gene sets.

Author information

1
Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
2
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
3
Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain.
4
CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain.
5
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona E-08010, Spain.
6
Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Barcelona E-08034, Spain.

Abstract

The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single protein isoform, the 'principal' isoform, as the reference for each gene based on these annotations. A single main splice isoform reflects the biological reality for most protein coding genes and APPRIS principal isoforms are the best predictors of these main proteins isoforms. Here, we present the updates to the database, new developments that include the addition of three new species (chimpanzee, Drosophila melangaster and Caenorhabditis elegans), the expansion of APPRIS to cover the RefSeq gene set and the UniProtKB proteome for six species and refinements in the core methods that make up the annotation pipeline. In addition APPRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets. The individual GENCODE/Ensembl, RefSeq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants.

PMID:
29069475
PMCID:
PMC5753224
DOI:
10.1093/nar/gkx997
[Indexed for MEDLINE]
Free PMC Article

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