LncTar protocols

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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 in pipelines

 (2)
2016
PMCID: 4940957
PMID: 27401977
DOI: 10.1186/s12864-016-2776-1

[…] rieseberg (university of british columbia) kindly gave us access. a hit with the genome was considered significant if the result had a bitscore ≥90 and an expected value e ≤ 10−6., software package ‘lnctar’ [] (version of september-01, 2015) was downloaded from site http://www.cuilab.cn/lnctar, and run in a subset of the sunflower lncrnas and meiotic genes. details of the procedure and results […]

2016
PMCID: 5308646
PMID: 27542205
DOI: 10.18632/oncotarget.11304

[…] profiles of the entire module and reflect the core functions of the module []. we used visant to visualize the gene connections (based on topological overlap) among the intramodular hub genes []., lnctar, a reliable bioinformatics tool, was used to analyze the interaction between hub lncrnas and hub coding genes in each module []. the variation on the standard “sliding” algorithm approach […]


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LncTar in publications

 (8)
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., differential expression analysis of de-mrna and de-lncrna in the two groups was performed using the deseq r […]

PMCID: 5575655
PMID: 28763026
DOI: 10.3390/genes8080191

[…] locus, the 100 kb upstream and downstream protein-coding genes (without overlap) were firstly identified as cis-acting target genes. then the genes that overlapped with the lncrnas predicted by lnctar (http://www.cuilab.cn/lnctar) were selected as trans-acting target genes. based on the target genes, lncrnas could be enriched in the candidate biological processes. , to analyze the main […]

PMCID: 5493346
PMID: 28665981
DOI: 10.1371/journal.pone.0180142

[…] show that ha117 promotes the characteristic stem-like signature of these cells by inhibiting by the ubiquitination and degradation of dnmt1 via its ability to down-regulate the ggl domain of rgs6., lnctar from the lnctar package (http://www.cuilab.cn/lnctar) [] was used to identify potential rna-rna interactions and binding sites between ha117 and rgs6. rna sequences and corresponding […]

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

[…] was within clinical mastitis qtl region. in addition, targeted genes for 10 lincrnas with the highest fragments per kilobase of transcript per million fragments mapped (fpkm) were predicted by lnctar for forecasting potential biological functions of these lincrnas. further analyses indicate involvement of lincrnas in several biological functions and different pathways., our study […]

PMCID: 5070814
PMID: 27760142
DOI: 10.1371/journal.pntd.0005069

[…] 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 […]


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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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