Wei2GO: weighted sequence similarity-based protein function prediction
Background Protein 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 la...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2022-02-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/12931.pdf |
| _version_ | 1797418852267589632 |
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| author | Maarten J.M.F. Reijnders |
| author_facet | Maarten J.M.F. Reijnders |
| author_sort | Maarten J.M.F. Reijnders |
| collection | DOAJ |
| description | Background Protein 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. Methods This 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. Results Wei2GO 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, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes. Availability Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO. |
| first_indexed | 2024-03-09T06:39:55Z |
| format | Article |
| id | doaj.art-20930d4872254c88a518077aeb290aa9 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:39:55Z |
| publishDate | 2022-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-20930d4872254c88a518077aeb290aa92023-12-03T10:52:36ZengPeerJ Inc.PeerJ2167-83592022-02-0110e1293110.7717/peerj.12931Wei2GO: weighted sequence similarity-based protein function predictionMaarten J.M.F. Reijnders0Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandBackground Protein 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. Methods This 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. Results Wei2GO 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, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes. Availability Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.https://peerj.com/articles/12931.pdfGene ontologyProtein functionsSequence similarityOpen sourceProteins |
| spellingShingle | Maarten J.M.F. Reijnders Wei2GO: weighted sequence similarity-based protein function prediction PeerJ Gene ontology Protein functions Sequence similarity Open source Proteins |
| title | Wei2GO: weighted sequence similarity-based protein function prediction |
| title_full | Wei2GO: weighted sequence similarity-based protein function prediction |
| title_fullStr | Wei2GO: weighted sequence similarity-based protein function prediction |
| title_full_unstemmed | Wei2GO: weighted sequence similarity-based protein function prediction |
| title_short | Wei2GO: weighted sequence similarity-based protein function prediction |
| title_sort | wei2go weighted sequence similarity based protein function prediction |
| topic | Gene ontology Protein functions Sequence similarity Open source Proteins |
| url | https://peerj.com/articles/12931.pdf |
| work_keys_str_mv | AT maartenjmfreijnders wei2goweightedsequencesimilaritybasedproteinfunctionprediction |