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miRseeker specifications


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


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

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

[…] 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, […]


Bioinformatic tools for microRNA dissection

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

[…] putative mirnas in genome sequences by targeting secondary rna structure, i.e. conserved hairpin structures that are characteristic of mirna precursor sequences in related species. mirscan () and mirseeker () are the main tools that target conserved intragenic sequences that can form hairpin structures based on rnafold and mfold, respectively. mirscan then compares the identified structures […]


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

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

[…] 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 []. […]


Novel Insights into miRNA in Lung and Heart Inflammatory Diseases

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

[…] 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 []. […]


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

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

[…] 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 […]


A Review of Computational Tools in microRNA Discovery

Front Genet
PMCID: 3654206
PMID: 23720668
DOI: 10.3389/fgene.2013.00081

[…] mirna discovery generally focused on the secondary structure of rna, looking for conserved hairpin structures between related species, such as srnaloop (grad et al., ), mirscan (lim et al., ), and mirseeker (lai et al., ). srnaloop is a tool based on sequence conservation and structure similarity that was used to predict mirnas from caenorhabditis elegans. this algorithm is similar to blast […]

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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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