ArticleProtein science : a publication of the Protein Society2022
PANNZER-A practical tool for protein function prediction.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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112 citing papers in PubMed.
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52 more citing papers are in PubMed but not listed here.
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Abstract
The facility of next-generation sequencing has led to an explosion of gene catalogs for novel genomes, transcriptomes and metagenomes, which are functionally uncharacterized. Computational inference has emerged as a necessary substitute for first-hand experimental evidence. PANNZER (Protein ANNotation with Z-scoRE) is a high-throughput functional annotation web server that stands out among similar publically accessible web servers in supporting submission of up to 100,000 protein sequences at once and providing both Gene Ontology (GO) annotations and free text description predictions. Here, we demonstrate the use of PANNZER and discuss future plans and challenges. We present two case studies to illustrate problems related to data quality and method evaluation. Some commonly used evaluation metrics and evaluation datasets promote methods that favor unspecific and broad functional classes over more informative and specific classes. We argue that this can bias the development of automated function prediction methods. The PANNZER web server and source code are available at http://ekhidna2.biocenter.helsinki.fi/sanspanz/.
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