Open AccessISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq
Author(s) -
Shuang Xie,
Yue Han,
Xiaozhou Chen,
Tai-Yu Cao,
Kai-Kai Ji,
Jie Zhu,
Ling Peng,
Chuan-Le Xiao
Publication year - 2018
Publication title -
international journal of genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.705
H-Index - 24
eISSN - 2314-4378
pISSN - 2314-436X
DOI - 10.1155/2018/9207637
Subject(s) - gene isoform , upload , computational biology , alternative splicing , sample (material) , gene , biology , database , focus (optics) , resource (disambiguation) , rna splicing , computer science , genetics , world wide web , rna , chromatography , optics , computer network , chemistry , physics
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.