ALDB: a domestic-animal long noncoding RNA database

Aimin Li; Junying Zhang; Zhongyin Zhou; Lei Wang; Yujuan Liu; Yajun Liu

doi:10.1371/journal.pone.0124003

ALDB: a domestic-animal long noncoding RNA database

PLoS One. 2015 Apr 8;10(4):e0124003. doi: 10.1371/journal.pone.0124003. eCollection 2015.

Authors

Aimin Li¹, Junying Zhang², Zhongyin Zhou³, Lei Wang⁴, Yujuan Liu⁵, Yajun Liu⁶

Affiliations

¹ School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, PR China; School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, PR China.
² School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, PR China.
³ Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, PR China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China.
⁴ School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, PR China.
⁵ Xi'an DongXing Branch, CMST Development Co. Ltd., Xi'an, Shaanxi, PR China.
⁶ School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, PR China; Higher Technology College, Xi'an University of Technology, Xi'an, Shaanxi, PR China.

Abstract

Background: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs.

Results: The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs.

Conclusions: ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Animals, Domestic
Cattle
Chickens / genetics*
Databases, Nucleic Acid*
Female
Molecular Sequence Annotation
Quantitative Trait Loci
RNA, Long Noncoding / classification
RNA, Long Noncoding / genetics*
Software*
Swine / genetics*

Substances

RNA, Long Noncoding

Grants and funding

This work was supported by the Natural Science Foundation of China (http://www.nsfc.gov.cn/) under Grants 61070137, 91130006, 61201312 and 61303122; and the Research Fund for the Doctoral Program of Higher Education of China (http://www.moe.edu.cn/, 20130203110017); and the Fundamental Research Funds for the Central Universities of China (http://www.moe.edu.cn/, BDY171416 and JB140306). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.