ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq
The accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using sing...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2018-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2018/9207637 |
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| author | Shang-Qian Xie Yue Han Xiao-Zhou Chen Tai-Yu Cao Kai-Kai Ji Jie Zhu Peng Ling Chuan-Le Xiao |
| author_facet | Shang-Qian Xie Yue Han Xiao-Zhou Chen Tai-Yu Cao Kai-Kai Ji Jie Zhu Peng Ling Chuan-Le Xiao |
| author_sort | Shang-Qian Xie |
| collection | DOAJ |
| description | The accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using single-molecule sequencing technologies, such as PacBio SMRT, provides long reads spanning entire transcript isoforms which do not require assembly. Therefore, we have developed ISOdb, a comprehensive resource database for hosting and carrying out an in-depth analysis of Iso-Seq datasets and visualising the full-length transcript isoforms. The current version of ISOdb has collected 93 publicly available Iso-Seq samples from eight species and presents the samples in two levels: (1) sample level, including metainformation, long read distribution, isoform numbers, and alternative splicing (AS) events of each sample; (2) gene level, including the total isoforms, novel isoform number, novel AS number, and isoform visualisation of each gene. In addition, ISOdb provides a user interface in the website for uploading sample information to facilitate the collection and analysis of researchers’ datasets. Currently, ISOdb is the first repository that offers comprehensive resources and convenient public access for hosting, analysing, and visualising Iso-Seq data, which is freely available. |
| format | Article |
| id | doaj-art-bd23e17b7ef64618be9f2b3ae86928d2 |
| institution | DOAJ |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-bd23e17b7ef64618be9f2b3ae86928d22025-08-20T03:23:19ZengWileyInternational Journal of Genomics2314-436X2314-43782018-01-01201810.1155/2018/92076379207637ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-SeqShang-Qian Xie0Yue Han1Xiao-Zhou Chen2Tai-Yu Cao3Kai-Kai Ji4Jie Zhu5Peng Ling6Chuan-Le Xiao7Research Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, ChinaSchool of Mathematics and Computer Science, Yunnan Minzu University, Kunming 650031, ChinaResearch Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaResearch Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaResearch Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaResearch Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, ChinaState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, ChinaThe accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using single-molecule sequencing technologies, such as PacBio SMRT, provides long reads spanning entire transcript isoforms which do not require assembly. Therefore, we have developed ISOdb, a comprehensive resource database for hosting and carrying out an in-depth analysis of Iso-Seq datasets and visualising the full-length transcript isoforms. The current version of ISOdb has collected 93 publicly available Iso-Seq samples from eight species and presents the samples in two levels: (1) sample level, including metainformation, long read distribution, isoform numbers, and alternative splicing (AS) events of each sample; (2) gene level, including the total isoforms, novel isoform number, novel AS number, and isoform visualisation of each gene. In addition, ISOdb provides a user interface in the website for uploading sample information to facilitate the collection and analysis of researchers’ datasets. Currently, ISOdb is the first repository that offers comprehensive resources and convenient public access for hosting, analysing, and visualising Iso-Seq data, which is freely available.http://dx.doi.org/10.1155/2018/9207637 |
| spellingShingle | Shang-Qian Xie Yue Han Xiao-Zhou Chen Tai-Yu Cao Kai-Kai Ji Jie Zhu Peng Ling Chuan-Le Xiao ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq International Journal of Genomics |
| title | ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq |
| title_full | ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq |
| title_fullStr | ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq |
| title_full_unstemmed | ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq |
| title_short | ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq |
| title_sort | isodb a comprehensive database of full length isoforms generated by iso seq |
| url | http://dx.doi.org/10.1155/2018/9207637 |
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