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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.


Screenshot of the BLAST and download pages.(A) The BLAST page. (B) The download page.
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pone.0124003.g005: Screenshot of the BLAST and download pages.(A) The BLAST page. (B) The download page.

Mentions: Since ALDB maintained nucleotide sequence data of lincRNAs, a sequence alignment tool, called wwwblast, based on the Basic Local Alignment Search Tool (BLAST) [43] was integrated into ALDB. Users can compare a query sequence with a library of lincRNA sequences using a BLAST search, and identify lincRNA sequences that closely resemble the query sequence. BLAST will meet users’ requirements for finding homologous transcripts or genes of interest. On the BLAST page (Fig 5A), users can supply one or more query sequences by uploading or directly pasting them to search against the available databases using BLAST’s default parameters. Users can also specify more parameters for a BLAST search to control its search sensitivity and result format, etc. The BLAST results will be displayed in another page in a pairwise format by default.


ALDB: a domestic-animal long noncoding RNA database.

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

Screenshot of the BLAST and download pages.(A) The BLAST page. (B) The download page.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0124003.g005: Screenshot of the BLAST and download pages.(A) The BLAST page. (B) The download page.
Mentions: Since ALDB maintained nucleotide sequence data of lincRNAs, a sequence alignment tool, called wwwblast, based on the Basic Local Alignment Search Tool (BLAST) [43] was integrated into ALDB. Users can compare a query sequence with a library of lincRNA sequences using a BLAST search, and identify lincRNA sequences that closely resemble the query sequence. BLAST will meet users’ requirements for finding homologous transcripts or genes of interest. On the BLAST page (Fig 5A), users can supply one or more query sequences by uploading or directly pasting them to search against the available databases using BLAST’s default parameters. Users can also specify more parameters for a BLAST search to control its search sensitivity and result format, etc. The BLAST results will be displayed in another page in a pairwise format by default.

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.