PANNZER2: a rapid functional annotation web server

By Petri Törönen, A. Medlar, Liisa Holm. Nucleic Acids Res., 2018

443 citations recorded by the source corpus.

Abstract The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f01827003f5a03cf015c030f00f8d9f1df9e3d05

How researchers see this paper

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In Molecular Biology

1. Aleksi Laiho
2. Marco Salgado
3. Petri Törönen
4. Liisa Holm
5. Laura M. Laakso
6. Johannes Söding

Citations in the corpus

• DALI and the persistence of protein shape (2019, background): “This is enabled by a fast sequence database search server,(35) which also powers function predictions by Pannzer2.(36) It is often useful to subject a set of top-scoring matches to all-against-all comparison.”
• DALI shines a light on remote homologs: One hundred discoveries (2022, methodology): “And if these were uninformative, we would additionally check: (i) Pannzer predictions (Törönen et al., 2018); (ii) the crystallographic literature at the RCSB site (https://www.”