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ALDB: a domestic-animal long noncoding RNA database.

Li A, Zhang J, Zhou Z, Wang L, Liu Y, Liu Y - PLoS ONE (2015)

Bottom Line: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes.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.A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


Visualization of genome annotation using GBrowse.(A) Users can search and browse features using GBrowse. (B) Detail page of a gene. (C) Tracks in GBrowse.
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pone.0124003.g003: Visualization of genome annotation using GBrowse.(A) Users can search and browse features using GBrowse. (B) Detail page of a gene. (C) Tracks in GBrowse.

Mentions: GBrowse greatly facilitates users to browse any region of interest in pig, chicken and cow genomes. It allows for a comprehensive analysis of the genomic neighborhood of a single gene or transcript. Users can select data source, and search transcripts or genes by their ids or names, or by a genomic region. A variety of track features can be accessed depending on the region’s position on the genomes, including lncRNA genes, protein-coding genes and QTLs (Fig 3A). In viewing the features, users can zooms out or zooms in a region to view the outline or details of a feature. If the user holds the cursor over a specified gene or transcript, a popup balloon will appear to show gene tracks, symbols and location information. Alternatively, by clicking on a specific gene, users can jump to a new corresponding gene information page to view its more considerable details (Fig 3B). Users can view different elements on different tracks by customizing tracks on the page “Select Tracks” (Fig 3C).


ALDB: a domestic-animal long noncoding RNA database.

Li A, Zhang J, Zhou Z, Wang L, Liu Y, Liu Y - PLoS ONE (2015)

Visualization of genome annotation using GBrowse.(A) Users can search and browse features using GBrowse. (B) Detail page of a gene. (C) Tracks in GBrowse.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390226&req=5

pone.0124003.g003: Visualization of genome annotation using GBrowse.(A) Users can search and browse features using GBrowse. (B) Detail page of a gene. (C) Tracks in GBrowse.
Mentions: GBrowse greatly facilitates users to browse any region of interest in pig, chicken and cow genomes. It allows for a comprehensive analysis of the genomic neighborhood of a single gene or transcript. Users can select data source, and search transcripts or genes by their ids or names, or by a genomic region. A variety of track features can be accessed depending on the region’s position on the genomes, including lncRNA genes, protein-coding genes and QTLs (Fig 3A). In viewing the features, users can zooms out or zooms in a region to view the outline or details of a feature. If the user holds the cursor over a specified gene or transcript, a popup balloon will appear to show gene tracks, symbols and location information. Alternatively, by clicking on a specific gene, users can jump to a new corresponding gene information page to view its more considerable details (Fig 3B). Users can view different elements on different tracks by customizing tracks on the page “Select Tracks” (Fig 3C).

Bottom Line: Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes.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.A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.