ArticlePeerJ2022
Wei2GO: weighted sequence similarity-based protein function prediction.
Article in PeerJ, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Toward next-generation therapeutic HPV vaccines: A review on expanding the antigen repertoire and an integrated bioinformatics selection framework.Human vaccines & immunotherapeutics · 2026Review
- Molecular and cellular insights into the parasitic infection of bloom-forming marine diatoms by Pirsonia diadema.Nature microbiology · 2026Article
- DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics.Frontiers in bioinformatics · 2025Article
- In silico protein function prediction: the rise of machine learning-based approaches.Medical review (2021) · 2023Review
- Article
- CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation.PLoS computational biology · 2022Article
- Convergent evolution of venom gland transcriptomes across Metazoa.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi.Environmental microbiology · 2021Article
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Authors and funding
1 author.
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Abstract
backgroundProtein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.
methodsThis paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.
resultsWei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, F AVAILABILITY: Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
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