LncTar statistics

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Citations per year

Number of citations per year for the bioinformatics software tool LncTar
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Tool usage distribution map

This map represents all the scientific publications referring to LncTar per scientific context
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Protocols

LncTar specifications

Information


Unique identifier OMICS_09348
Name LncTar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Output data Paired RNAs
Output format TXT
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_09348
Name LncTar
Interface Web user interface
Restrictions to use None
Input data A LncRNA or RNA sequence
Input format FASTA
Output data Paired RNAs
Output format TXT
Computer skills Basic
Stability Stable
Maintained Yes

Publication for LncTar

LncTar citations

 (5)
library_books

Genome wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep

2018
Biosci Rep
PMCID: 5920141
PMID: 29439142
DOI: 10.1042/BSR20171350

[…] genes, which can be predicted based on the position of lncRNA and mRNA, and adjacent genes within a range of 100 kb of its target gene. Second, lncRNA and mRNA function through base pairing, and the LncTar [] target gene prediction tool was used to predict the target gene of lncRNA. […]

library_books

Identification and characterization of long intergenic noncoding RNAs in bovine mammary glands

2017
BMC Genomics
PMCID: 5477121
PMID: 28629368
DOI: 10.1186/s12864-017-3858-4

[…] In order to predict the targets of lincRNAs in mammary glands and thus understand potential functions of lincRNAs, the LncTar tool with the first type of file format for predicting the lincRNA–RNA interactions was used. The first type of file format contains two files. One file was lincRNA sequence file and the other […]

library_books

Non Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non Invasive Diagnostic Tools

2016
Genes
PMCID: 5295003
PMID: 28035947
DOI: 10.3390/genes8010008

[…] rable with existing algorithms but significantly faster, however it has room for further improvements to reach higher accuracy especially for lncRNA interaction predictions []. On the other hand, the LncTar software allows calculation of lncRNA-RNA interactions in large-scale datasets []. It assumes that the primer-dimer detection is not only important for real-time polymerase chain reaction (PCR) […]

call_split

Identification of Aedes aegypti Long Intergenic Non coding RNAs and Their Association with Wolbachia and Dengue Virus Infection

2016
PLoS Negl Trop Dis
PMCID: 5070814
PMID: 27760142
DOI: 10.1371/journal.pntd.0005069
call_split See protocol

[…] :U pairing in the seed region (nucleotide 2–8) and required miRNA-lincRNA duplexes to have a helix in this region. Maximum 5nt were allowed as unpaired nucleotides in either side of an internal loop. LncTar algorithm [] was used to explore any potential interaction between lincRNA_1317 and DENV-2 genome (accession no. NC_001474.2) by finding the normalized mfe joint structure of two RNA molecules […]

library_books

lncRNA RNA Interactions across the Human Transcriptome

2016
PLoS One
PMCID: 4773119
PMID: 26930590
DOI: 10.1371/journal.pone.0150353

[…] es the task infeasible. In a test that we performed on a sample of 1000 randomly selected lncRNAs-RNA pairs, it took 25.6 minutes for RNAplex [], 23.43 minutes for RNAduplex [], and 70.50 minutes for LncTar [] to calculate RNA-RNA interactions, so by extrapolation it would take 1,552, 1,421, and 4.276 years, respectively, to find interactions between all considered components (215,170 lncRNAs vers […]


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LncTar institution(s)
Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China; School of Computer Science, Hebei University of Technology, Tianjin, China
LncTar funding source(s)
This study was supported by National Nature Science Foundation of China (Nos. 91339106, 81422006) and the 863 project (2014AA021102).

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