R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It include...
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| Format: | Journal Article |
| Language: | English |
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2017
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| Online Access: | https://hdl.handle.net/10356/81411 http://hdl.handle.net/10220/43467 |
| _version_ | 1824453619584335872 |
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| author | Jenjaroenpun, Piroon Wongsurawat, Thidathip Sutheeworapong, Sawannee Kuznetsov, Vladimir A. |
| author2 | School of Computer Science and Engineering |
| author_facet | School of Computer Science and Engineering Jenjaroenpun, Piroon Wongsurawat, Thidathip Sutheeworapong, Sawannee Kuznetsov, Vladimir A. |
| author_sort | Jenjaroenpun, Piroon |
| collection | NTU |
| description | R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1 565 795 RLFSs distributed in 121 056 genic or proximal gene regions of the covered organisms. It provides a comprehensive annotation of Ensembl RLFS-positive genes including 93 454 protein coding genes, 12 480 long non-coding RNA and 7 568 small non-coding RNA genes and 7 554 pseudogenes. Using new interface and genome viewers of R-loopDB, users can search the gene(s) in multiple species with keywords in a single query. R-loopDB provides tools to carry out comparative evolution and genome-scale analyses in R-loop biology. |
| first_indexed | 2025-02-19T03:09:18Z |
| format | Journal Article |
| id | ntu-10356/81411 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:09:18Z |
| publishDate | 2017 |
| record_format | dspace |
| spelling | ntu-10356/814112020-03-07T11:48:55Z R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops Jenjaroenpun, Piroon Wongsurawat, Thidathip Sutheeworapong, Sawannee Kuznetsov, Vladimir A. School of Computer Science and Engineering Chromosomes Genes R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1 565 795 RLFSs distributed in 121 056 genic or proximal gene regions of the covered organisms. It provides a comprehensive annotation of Ensembl RLFS-positive genes including 93 454 protein coding genes, 12 480 long non-coding RNA and 7 568 small non-coding RNA genes and 7 554 pseudogenes. Using new interface and genome viewers of R-loopDB, users can search the gene(s) in multiple species with keywords in a single query. R-loopDB provides tools to carry out comparative evolution and genome-scale analyses in R-loop biology. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version 2017-07-27T06:59:26Z 2019-12-06T14:30:24Z 2017-07-27T06:59:26Z 2019-12-06T14:30:24Z 2016 Journal Article Jenjaroenpun, P., Wongsurawat, T., Sutheeworapong, S., & Kuznetsov, V. A. (2017). R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. Nucleic Acids Research, 45(D1), D119-D127. 0305-1048 https://hdl.handle.net/10356/81411 http://hdl.handle.net/10220/43467 10.1093/nar/gkw1054 en Nucleic Acids Research © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. 9 p. application/pdf |
| spellingShingle | Chromosomes Genes Jenjaroenpun, Piroon Wongsurawat, Thidathip Sutheeworapong, Sawannee Kuznetsov, Vladimir A. R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops |
| title | R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops |
| title_full | R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops |
| title_fullStr | R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops |
| title_full_unstemmed | R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops |
| title_short | R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops |
| title_sort | r loopdb a database for r loop forming sequences rlfs and r loops |
| topic | Chromosomes Genes |
| url | https://hdl.handle.net/10356/81411 http://hdl.handle.net/10220/43467 |
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