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Generation of Comprehensive Thoracic Oncology Database - Tool for Translational Research

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Published on: January 22, 2011

ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq.

Shang-Qian Xie¹, Yue Han², Xiao-Zhou Chen³

¹Research Center for Terrestrial Biodiversity of the South China Sea, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.

International Journal of Genomics

|December 25, 2018

Summary

ISOdb is a new database for analyzing full-length transcript isoforms using Iso-Seq long-read data. It offers comprehensive resources for hosting, analyzing, and visualizing Iso-Seq datasets across multiple species.

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The ITS2 Database

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Published on: March 12, 2012

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The ITS2 Database

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Published on: March 12, 2012

Area of Science:

Genomics
Transcriptomics
Bioinformatics

Background:

Accurate transcript isoform identification is crucial for understanding gene function and regulation.
Short-read sequencing technologies present challenges in assembling complete transcript isoforms.
Isoform sequencing (Iso-Seq) with long-read technologies offers a solution for capturing full-length transcripts without assembly.

Purpose of the Study:

To develop ISOdb, a comprehensive database for hosting, analyzing, and visualizing Iso-Seq datasets.
To provide a centralized resource for researchers studying transcript isoforms.
To facilitate the collection and analysis of new Iso-Seq data.

Main Methods:

Collected 93 publicly available Iso-Seq samples from eight species.
Organized data into sample-level (metainformation, read distribution, AS events) and gene-level (isoform counts, novel isoforms/AS, visualization) views.
Developed a user interface for uploading and analyzing custom datasets.

Main Results:

ISOdb currently hosts data from 93 Iso-Seq samples across eight species.
The database provides detailed analysis at both sample and gene levels, including novel isoform and alternative splicing event identification.
A user-friendly interface is available for data submission and analysis.

Conclusions:

ISOdb is the first repository offering comprehensive resources for hosting, analyzing, and visualizing Iso-Seq data.
The database provides valuable insights into transcript isoform diversity and alternative splicing.
ISOdb is freely available, promoting accessibility and advancing transcriptomics research.