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MiRAlign specifications


Unique identifier OMICS_07324
Name MiRAlign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for MiRAlign

MiRAlign citations


A Review on Recent Computational Methods for Predicting Noncoding RNAs

Biomed Res Int
PMCID: 5434267
PMID: 28553651
DOI: 10.1155/2017/9139504

[…] , which make this RNA relatively conserved in secondary structure. Thus, a few methods exploit more secondary features for new miRNA gene detection instances. For example, as a homology-based method, miRAlign employs sequence alignment, secondary structure alignment, and miRNA's position on the stem-loop structure to identify RNA homologs. It has higher sensitivity and comparable specificity than […]


Identification of Known and Novel microRNAs and Their Targets in Peach (Prunus persica) Fruit by High Throughput Sequencing

PLoS One
PMCID: 4965121
PMID: 27466805
DOI: 10.1371/journal.pone.0159253

[…] To identify known miRNAs in peach fruit, the candidate peach miRNA sequences were aligned with the newly released mature plant miRNAs in miRBase 18.0 [] using miRAlign (BGI). The expression profiles of these miRNAs are presented in . In total, 557 known miRNAs belonging to 34 miRNA families were identified in the library of peach fruit. Various miRNAs were […]


Composition and genomic organization of arthropod Hox clusters

PMCID: 4862073
PMID: 27168931
DOI: 10.1186/s13227-016-0048-4

[…] ides and greater than or equal to 80 percent identity (Additional file : Table┬áS4). BLAST hits were then analyzed for predicted secondary structure using minimum free energy (MFE) with RNAfold [] and miRAlign []. Only sequences with a predicted stem-loop structure with a MFE less than or equal to -20┬ákcal/mol and that contained the mature sequence on the stem were considered putative miRNAs (Addit […]


Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution

Front Physiol
PMCID: 4620411
PMID: 26578966
DOI: 10.3389/fphys.2015.00286
call_split See protocol

[…] nine putative miRs were identified in wheat using traditional computational strategy, out of which 9 were validated by northern blot experiments (Jin et al., ). Subsequently bioinformatics tools like miRAlign were developed based on the requirement of structural similarity and sequence conservation between new candidates and experimentally identified miRs (Wang et al., ). Though numerous miR profi […]


The expression profile of Aedes albopictus miRNAs is altered by dengue virus serotype 2 infection

PMCID: 4411651
PMID: 25922662
DOI: 10.1186/s13578-015-0009-y

[…] ismatches; the secondary structures of the hairpins were stable, with free energies of hybridization lower than -20 kcal/mol; and hairpins were located in intergenic regions or introns. Subsequently, miRAlign was adopted to filter mature miRNA genes and predict new miRNA genes, and each novel miRNA in the samples was required to have at least 15 reads to be considered as expressed. The whole proce […]


A Complex Genome MicroRNA Interplay in Human Mitochondria

Biomed Res Int
PMCID: 4324738
PMID: 25695052
DOI: 10.1155/2015/206382

[…] Total 110 miRNA candidate sequences were scanned to find out real versus false miRNA. Three types of software were used for proper identification of miRNA. These types of software are MiPred, MiRAlign, and Mireval. MiPred. The MiPred web server (http://www.bioinf.seu.edu.cn/miRNA/) was used to distinguish the real pre-miRNA from other hairpin sequences with similar stem-loops (pseudo pre-m […]

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MiRAlign institution(s)
MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing, China

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