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miRseeker specifications

Information


Unique identifier OMICS_07335
Name miRseeker
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Database management system MySQL
Computer skills Advanced
Stability No
Maintained No

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Publication for miRseeker

miRseeker citations

 (19)
library_books

MicroRNA: Biological and Computational Perspective

2016
PMCID: 5172550
PMID: 16393143
DOI: 10.1016/S1672-0229(05)03011-1

[…] iRNA genes in various species, including C. elegans , , , D. melanogaster , human , , , , , Arabidopsis and other plants , , , , and virus , . Two of the programs developed to predict miRNA genes are MiRseeker and MiRscan , , .Methods to find miRNA genes computationally usually utilize the following properties of known miRNA genes:1. The precursor of miRNAs can form stable extended stem-loop stru […]

library_books

Well characterized sequence features of eukaryote genomes and implications for ab initio gene prediction

2016
Comput Struct Biotechnol J
PMCID: 4975701
PMID: 27536341
DOI: 10.1016/j.csbj.2016.07.002

[…] ates of miRNA genes, which could be computationally deduced on basis of the estimated free energy by tools of RNAfold and Mfold . Actually, the homology search-based approaches, such as MiRscan and miRseeker , were also designed to first scan intergenic regions of entire genome and generate full list of candidates according to the deduced hairpin sequences before homology search. Therefore, desi […]

library_books

Bioinformatic tools for microRNA dissection

2015
Nucleic Acids Res
PMCID: 4705652
PMID: 26578605
DOI: 10.1093/nar/gkv1221

[…] e identified structures with known miRNA features like 3′ and 5′-stem conservation, whereas miRseeker selects hairpins sharing similar nucleotide divergence patterns to the reference set. MiRscan and miRseeker were first applied to identify miRNAs in nematodes and flies, respectively, and a large number of predicted candidates were then validated experimentally.However, since tools based on compar […]

library_books

Identification of a novel miRNA from the ovine ovary by a combinatorial approach of bioinformatics and experiments

2015
PMCID: 4710718
PMID: 26268666
DOI: 10.1292/jvms.15-0289

[…] Compared with traditional methods, high-throughput sequencing technology has a specific advantage for discovery of novel miRNAs with particular function . Many computational programs, such as miRSan, miRseeker, Mfold and findMiRNA, have been used for predicting unknown miRNAs [], and these programs are based on minimal free energies and specific miRNA hairpin stem-loop structures []. In this study […]

library_books

Novel Insights into miRNA in Lung and Heart Inflammatory Diseases

2014
PMCID: 4058468
PMID: 24991086
DOI: 10.1155/2014/259131

[…] dely adopted []. In the process of identification of miRNAs, several computational approaches have been developed that complement the experimental analysis. These in silico resources include MiRscam, miRSeeker, Phylogenetic shadowing, miRank, miRDeep, MiRanalyzer, proMiR II, mir-abela, triplet-SVM, Vmir, RNA micro, BayesMiRNAFind, One-ClassMirnaFind, miPred, Srnaloop, and findMiRNA []. Additionall […]

library_books

Antiviral Stratagems Against HIV 1 Using RNA Interference (RNAi) Technology

2013
Evol Bioinform Online
PMCID: 3662398
PMID: 23761954
DOI: 10.4137/EBO.S11412

[…] refore thought that miRNAs play a very crucial role in cancers and a series of other as important human diseases. Existing widely used computational methods, such as MiRscan,, miRAlign, Srnaloop, and miRseeker for miRNA, prediction in animals and plants rely heavily on sequence and/ or structural phylogenetic conservation. However, as opposed to animal and plant miRNAs, viral miRNAs lack conservat […]

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miRseeker institution(s)
Supported by a grant from the Damon Runyon Cancer Research Fund (DRG 1632) and by the Howard Hughes Medical Institute.

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