SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability
RNA secondary structures can carry out essential cellular functions alone or interact with one another to form the hierarchical tertiary structures. Experimental structure identification approa ches can show the in vitro structures of RNA molecules. However, they usually have limits in the resolutio...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022001842 |
| _version_ | 1797978211002351616 |
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| author | Tzu-Hsien Yang Yu-Cian Lin Min Hsia Zhan-Yi Liao |
| author_facet | Tzu-Hsien Yang Yu-Cian Lin Min Hsia Zhan-Yi Liao |
| author_sort | Tzu-Hsien Yang |
| collection | DOAJ |
| description | RNA secondary structures can carry out essential cellular functions alone or interact with one another to form the hierarchical tertiary structures. Experimental structure identification approa ches can show the in vitro structures of RNA molecules. However, they usually have limits in the resolution and are costly. In silico structure prediction tools are thus primarily relied on for pre-experiment analysis. Various structure prediction models have been developed over the decades. Since these tools are usually used before knowing the actual RNA structures, evaluating and ranking the pile of secondary structure predictions of a given sequence is essential in computational analysis. In this research, we implemented a web service called SSRTool (RNA Secondary Structure prediction Ranking Tool) to assist in the ranking and evaluation of the generated predicted structures of a given sequence. Based on the computed species-specific interpretability significance in four common RNA structure–function aspects, SSRTool provides three functions along with visualization interfaces: (1) Rank user-generated predictions. (2) Provide an automated streamline of structure prediction and ranking for a given sequence. (3) Infer the functional aspects of a given structure. We demonstrated the applicability of SSRTool via real case studies and reported the similar trends between computed species-specific rankings and the corresponding prediction F1 values. The SSRTool web service is available online at https://cobisHSS0.im.nuk.edu.tw/SSRTool/, http://cosbi3.ee.ncku.edu.tw/SSRTool/, or the redirecting site https://github.com/cobisLab/SSRTool/. |
| first_indexed | 2024-04-11T05:19:23Z |
| format | Article |
| id | doaj.art-4414daea991b4876abdcb5c62e281555 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:23Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-4414daea991b4876abdcb5c62e2815552022-12-24T04:52:32ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012024732483SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretabilityTzu-Hsien Yang0Yu-Cian Lin1Min Hsia2Zhan-Yi Liao3Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan; Corresponding author.Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, TaiwanDepartment of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, TaiwanDepartment of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, TaiwanRNA secondary structures can carry out essential cellular functions alone or interact with one another to form the hierarchical tertiary structures. Experimental structure identification approa ches can show the in vitro structures of RNA molecules. However, they usually have limits in the resolution and are costly. In silico structure prediction tools are thus primarily relied on for pre-experiment analysis. Various structure prediction models have been developed over the decades. Since these tools are usually used before knowing the actual RNA structures, evaluating and ranking the pile of secondary structure predictions of a given sequence is essential in computational analysis. In this research, we implemented a web service called SSRTool (RNA Secondary Structure prediction Ranking Tool) to assist in the ranking and evaluation of the generated predicted structures of a given sequence. Based on the computed species-specific interpretability significance in four common RNA structure–function aspects, SSRTool provides three functions along with visualization interfaces: (1) Rank user-generated predictions. (2) Provide an automated streamline of structure prediction and ranking for a given sequence. (3) Infer the functional aspects of a given structure. We demonstrated the applicability of SSRTool via real case studies and reported the similar trends between computed species-specific rankings and the corresponding prediction F1 values. The SSRTool web service is available online at https://cobisHSS0.im.nuk.edu.tw/SSRTool/, http://cosbi3.ee.ncku.edu.tw/SSRTool/, or the redirecting site https://github.com/cobisLab/SSRTool/.http://www.sciencedirect.com/science/article/pii/S2001037022001842RNA secondary structureRNA structure prediction evaluationRNA functional interpretability |
| spellingShingle | Tzu-Hsien Yang Yu-Cian Lin Min Hsia Zhan-Yi Liao SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability Computational and Structural Biotechnology Journal RNA secondary structure RNA structure prediction evaluation RNA functional interpretability |
| title | SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability |
| title_full | SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability |
| title_fullStr | SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability |
| title_full_unstemmed | SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability |
| title_short | SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability |
| title_sort | ssrtool a web tool for evaluating rna secondary structure predictions based on species specific functional interpretability |
| topic | RNA secondary structure RNA structure prediction evaluation RNA functional interpretability |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022001842 |
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