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Sylamer specifications


Unique identifier OMICS_20463
Name Sylamer
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.5
Stability Stable
Source code URL
Maintained Yes




No version available


  • person_outline Anton Enright <>

Publication for Sylamer

Sylamer citations


TGF β induces miR 100 and miR 125b but blocks let 7a through LIN28B controlling PDAC progression

PMCID: 5945639
PMID: 29748571
DOI: 10.1038/s41467-018-03962-x

[…] developed a novel approach to integrate mirna overexpression with ago2 rna immunoprecipitation (rip) sequencing (rip-seq) and differential expression analysis within a bioinformatics framework with sylamer and cwords algorithms–. we called this method rip followed by unbiased sequence enrichment analysis (rip-use) (fig.  and methods). this method is developed in several steps (fig. ), including […]


Molecular mechanism of diabetic cardiomyopathy and modulation of microRNA function by synthetic oligonucleotides

PMCID: 5863891
PMID: 29566757
DOI: 10.1186/s12933-018-0684-1

[…] on alternative splicing, rna editing and post-transcriptional modification []. additionally, an alternative and impartial method of analyzing the effect of mir perturbation is to use the “sylamer algorithm” [] that uses expression changes measured after, for example, mir silencing to rank genes and subsequently test the occurrence of all possible sequence motifs of a given length […]


A mouse model of miR 96, miR 182 and miR 183 misexpression implicates miRNAs in cochlear cell fate and homeostasis

PMCID: 5824881
PMID: 29476110
DOI: 10.1038/s41598-018-21811-1

[…] effects at p18. alternatively, the mirna/mrna interactions could include non-conserved and/or off-target effects of the mir-183 cluster. to address the latter two possibilities, we employed the sylamer program to identify, through hypergeometric analysis, over- or under-represented 7-mer sequence strings (seeds) in the mouse 3′utr transcriptome interrogated by the affymetrix mogene 1.0 […]


MicroRNAs and Presbycusis

PMCID: 5772851
PMID: 29392088
DOI: 10.14336/AD.2017.0119

[…] mouse with mutation of mir-96 was used to study the function of mirna-96 in the inner ear []. the mutant, named diminuendo, has an a>t substitution in the seed region of mir-96. sylamer analysis indicated that the mutation had both direct and indirect effects on expression of many genes. utilizing the miranda target predictor v3.0 and luciferase assay, five mrnas […]


High content image analysis reveals function of miR 124 upstream of Vimentin in regulating motor neuron mitochondria

PMCID: 5758812
PMID: 29311649
DOI: 10.1038/s41598-017-17878-x

[…] profile for neurons that overexpressed mir-124, which was distinguishable from cells transfected with scrambled control oligos (dendrogram of pearson correlation coefficient, fig. ).figure 2 , sylamer analysis of 6500 expressed mrnas, from neurons expressing scrambled control mimics or mir-124, uncovered two enriched motifs, which matched the mir-124 ‘seed’ sequence. however, […]


Intron retention enhances gene regulatory complexity in vertebrates

PMCID: 5688624
PMID: 29141666
DOI: 10.1186/s13059-017-1339-3

[…] (additional file : figure s16)., in addition, we identified significantly over-represented sequence motifs (putative mirna seed sites) in the 3′ utr sequences of intron-retaining genes using sylamer []. interestingly, we found strong similarities among the enriched sequence motifs in mammalian species (fig. ; additional file : figure s17 and table s4) and the motifs are, on average, […]

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Sylamer institution(s)
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Sylamer funding source(s)
Supported by the Wellcome Trust.

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