SSCprofiler

SSC (Sequence, Structure and Conservation) profiler is running on a server in Poirazi Lab at the Institute of Molecular Biology and Biotechnology (IMBB), FoRTH, Heraklion, Greece. For more details see the reference denoted below.

SSCprofiler works using human genomic coordinates (version - hg17). By selecting the chromosome number and the start and end nucleotides, it is possible to scan specific genomic regions for miRNA genes. SSCprofiler also provides a link to the full genome tilling array RNA expression map published by Kapranov et al. Science 316, 2007

The Filtering parameters can be defined below. The default parameters are as defined in the human miRNA gene prediction analysis performed in the SSCprofiler paper.

Important note: This web interface is limited to sequences up to 1kb.

Oulas et al. 2009. Prediction of novel microRNA genes in cancer-associated genomic regions -- a combined computational and experimental approach. Nucleic Acids Res 37(10):3276-87. doi: 10.1093/nar/gkp120. Epub 2009 Mar 25. PMID: 19324892; PMCID: PMC2691815.

Chromosome:

Start:

End:

Strand:

Expression:

Choose a file to upload: Help?

Expression Threshold:

HMM Threshold:

Filters:

Free Energy:

Hairpin Count:

Bulge Count:

Loop Count:

Side Symmetry:

Loop + Bulge count:

Hairpin Size:

Conservation:

For questions, comments and feedback regarding Targetprofiler, please contact Panayiota Poirazi (software [AT] dendrites [DOT] gr)