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SiLoCo specifications


Unique identifier OMICS_14631
Name SiLoCo
Alternative name Short interfering RNA Locus Comparison
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
Computer skills Medium
Version 2.0
Stability No
Maintained No




No version available


This tool is not available anymore.

Publication for Short interfering RNA Locus Comparison

SiLoCo citations


Considerations and complications of mapping small RNA high throughput data to transposable elements

PMCID: 5311732
PMID: 28228849
DOI: 10.1186/s13100-017-0086-z

[…] reviewed in []) using different approaches and sRNA analysis tools. For example, the NiBLS method allows multiple mapping without any kind of normalization for the number of mapping locations [], the SiLoCo tool of the UEA sRNA Toolkit weights each read by its repetitiveness in the genome [], the segmentSeq package of Bioconductor allocates each M_sRNA only once to a predefined locus even if it ma […]


The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages

Sci Rep
PMCID: 5286533
PMID: 28145468
DOI: 10.1038/srep41052

[…] R) for targeting the four rice AGO1 homologs such as AGO1a, b, c, and d. The relative position of srRNAs in the selected libraries was determined by mapping the reads to ribosomal RNA using PatMaN in SiLoCo and VisSR Tool of UEA small RNA workbench ( The srRNAs were analyzed for their length distribution pattern and cleavage around the unique signature motif. The read […]


The germline of the malaria mosquito produces abundant miRNAs, endo siRNAs, piRNAs and 29 nt small RNAs

BMC Genomics
PMCID: 4345017
PMID: 25766668
DOI: 10.1186/s12864-015-1257-2

[…] U as first nucleotide or an adenosine A at the 10th position were bioinformatically selected from each sample in order to enrich the reads of piRNAs. Clusters of piRNAs were than identified using the SiLoCo implementation from the UEA small RNA Workbench [], considering chromosomal regions no larger than 100 base pairs (bp), loci containing average read size that range from 26 to 27 and containing […]


Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data

PMCID: 4009774
PMID: 24832228
DOI: 10.3390/biology1020297

[…] UEA sRNA Toolkit [] combines two integrated parts, miRCat and SiLoCo, to analyze miRNAs using deep sequencing data. miRCat, the package for detecting miRNAs, adopts a number of empirical and published criteria for bona fide miRNA loci to mine miRNAs from deeply […]


Genome wide profiling of Populus small RNAs

BMC Genomics
PMCID: 2811130
PMID: 20021695
DOI: 10.1186/1471-2164-10-620

[…] The redundant sequence data was used as input for the siLoCo and ta-siRNA prediction tools. For these tools, all options were left at their defaults. A p value of 0.001 was used for the ta-siRNA prediction tool. The output from the ta-siRNA prediction to […]


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SiLoCo institution(s)
School of Computing Sciences, University of East Anglia, Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK; The Sainsbury Laboratory, Norwich, UK
SiLoCo funding source(s)
This work was supported by the Biotechnology and Biological Sciences Research Council [grant number BB/E004091/1] and the Gatsby Charitable Foundation.

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