STADIUM: Species-Specific tRNA Adaptive Index Compendium
Due to the increasing interest in synonymous codons, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago. The tAI is a measure of translational efficiency for a gene and is calculated based on the abundance of intr...
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| Language: | English |
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e28.pdf |
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| author | Jonghwan Yoon Yeun-Jun Chung Minho Lee |
| author_facet | Jonghwan Yoon Yeun-Jun Chung Minho Lee |
| author_sort | Jonghwan Yoon |
| collection | DOAJ |
| description | Due to the increasing interest in synonymous codons, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago. The tAI is a measure of translational efficiency for a gene and is calculated based on the abundance of intracellular tRNA and the binding strength between a codon and a tRNA. The index has been widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, an improved version of the index, named specific tRNA adaptation index (stAI), was developed by adapting tRNA copy numbers in species. Although a subsequently developed webserver (stAIcalc) provided tools that calculated stAI values, it was not available to access pre-calculated values. In addition to about 100 species in stAIcalc, we calculated stAI values for whole coding sequences in 148 species. To enable easy access to this index, we constructed a novel web database, named STADIUM (Species-specific tRNA adaptive index compendium). STADIUM provides not only the stAI value of each gene but also statistics based on pathway-based classification. The database is expected to help researchers who have interests in codon optimality and the role of synonymous codons. STADIUM is freely available at http://stadium.pmrc.re.kr. |
| format | Article |
| id | doaj-art-71ef0271538340e6af1ea33d2865ab06 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-71ef0271538340e6af1ea33d2865ab062025-02-02T04:14:06ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e28530STADIUM: Species-Specific tRNA Adaptive Index CompendiumJonghwan Yoon0Yeun-Jun Chung1Minho Lee2 Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, KoreaDue to the increasing interest in synonymous codons, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago. The tAI is a measure of translational efficiency for a gene and is calculated based on the abundance of intracellular tRNA and the binding strength between a codon and a tRNA. The index has been widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, an improved version of the index, named specific tRNA adaptation index (stAI), was developed by adapting tRNA copy numbers in species. Although a subsequently developed webserver (stAIcalc) provided tools that calculated stAI values, it was not available to access pre-calculated values. In addition to about 100 species in stAIcalc, we calculated stAI values for whole coding sequences in 148 species. To enable easy access to this index, we constructed a novel web database, named STADIUM (Species-specific tRNA adaptive index compendium). STADIUM provides not only the stAI value of each gene but also statistics based on pathway-based classification. The database is expected to help researchers who have interests in codon optimality and the role of synonymous codons. STADIUM is freely available at http://stadium.pmrc.re.kr.http://genominfo.org/upload/pdf/gi-2018-16-4-e28.pdfcodon optimalityKEGG pathwayShinytRNA adaptive index |
| spellingShingle | Jonghwan Yoon Yeun-Jun Chung Minho Lee STADIUM: Species-Specific tRNA Adaptive Index Compendium Genomics & Informatics codon optimality KEGG pathway Shiny tRNA adaptive index |
| title | STADIUM: Species-Specific tRNA Adaptive Index Compendium |
| title_full | STADIUM: Species-Specific tRNA Adaptive Index Compendium |
| title_fullStr | STADIUM: Species-Specific tRNA Adaptive Index Compendium |
| title_full_unstemmed | STADIUM: Species-Specific tRNA Adaptive Index Compendium |
| title_short | STADIUM: Species-Specific tRNA Adaptive Index Compendium |
| title_sort | stadium species specific trna adaptive index compendium |
| topic | codon optimality KEGG pathway Shiny tRNA adaptive index |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e28.pdf |
| work_keys_str_mv | AT jonghwanyoon stadiumspeciesspecifictrnaadaptiveindexcompendium AT yeunjunchung stadiumspeciesspecifictrnaadaptiveindexcompendium AT minholee stadiumspeciesspecifictrnaadaptiveindexcompendium |