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Protocols

SSCprofiler specifications

Information


Unique identifier OMICS_02055
Name SSCprofiler
Alternative name Sequence, Structure and Conservation profiler
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Sequence, Structure and Conservation profiler

SSCprofiler citations

 (3)
library_books

Bioinformatic tools for microRNA dissection

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

[…] volutionary conservation. The method implements a hierarchical HMM that utilizes region-based structural as well as sequence information of miRNA precursors. Another freely available prediction tool, SSCprofiler (,), harnesses a probabilistic method based on Profile HMMs, trained to recognize key biological miRNA features such as sequence, structure and conservation, to identify novel miRNA precur […]

call_split

MicroRNAs: New Biomarkers for Diagnosis, Prognosis, Therapy Prediction and Therapeutic Tools for Breast Cancer

2015
Theranostics
PMCID: 4508501
PMID: 26199650
DOI: 10.7150/thno.11543
call_split See protocol

[…] ing sets . Many tools of machine learning-based approaches for miRNA target prediction are currently available, e.g., HHMMiR , PicTar , MiRFinder , RNAmicro , , ProMiR , MiRRim , BayesMiRNAFind , and SSCprofiler .Other computational algorithms use approaches different from machine learning. The TargetScan algorithm was the first miRNA target prediction tool for human genome . It searches for perfe […]

library_books

A Review of Computational Tools in microRNA Discovery

2013
Front Genet
PMCID: 3654206
PMID: 23720668
DOI: 10.3389/fgene.2013.00081

[…] The commonly used tools among the methods directed to predict miRNAs from NGS data include miRDeep (Friedlander et al., ), miRanalyzer (Hackenberg et al., ), and SSCprofiler (Oulas et al., ). MiRDeep is able to discover previously known miRNAs as well as novel ones by using properties of miRNA biogenesis to score the compatibility of the position and frequency […]

Citations

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SSCprofiler institution(s)
Institute of Molecular Biology and Biotechnology-FORTH, Heraklion, University of Crete, Heraklion, Greece

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