SISSIz statistics

info info

Citations per year


Tool usage distribution map

info info

Associated diseases


Popular tool citations

chevron_left Structure alignment chevron_right
Want to access the full stats & trends on this tool?

SISSIz specifications


Unique identifier OMICS_14952
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.1
Stability Stable
Maintained Yes




No version available



  • person_outline Stefan Washietl

Publication for SISSIz

SISSIz citations


Mutation pattern is an influential factor on functional mutation rates in cancer

PMCID: 4748466
PMID: 26865835
DOI: 10.1186/s12935-016-0278-5

[…] 117 were identified through alignment of 46 mammalian genomes with human []. Evolutionarily conserved structures (ECS) are RNA secondary structures predicted with a nouvel pipeline based on RNAz and SISSIz in Smith MA’ study []. Promoters generated by the Gerstein lab are regulatory regions 2.5 Kb from transcription start sites (TSS) []. Genome-wide mapping of histone acetylation and methylation […]


RNA 3D Modules in Genome Wide Predictions of RNA 2D Structure

PLoS One
PMCID: 4624896
PMID: 26509713
DOI: 10.1371/journal.pone.0139900

[…] tides, but then the other five sequences match a really small JAR3D module well. It is surprising that such situations appear to occur more often in original windows than in shuffled windows, because SISSIz is designed to preserve the gap distribution.When the secondary structure is predicted reliably and we can extract the correct loop regions, the use of JAR3D for the 3D module prediction is pre […]


Long Non Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer Related Protein Coding Genes

PLoS One
PMCID: 4180073
PMID: 25264628
DOI: 10.1371/journal.pone.0106076

[…] d small RNAs (, ). Non-coding DE-probes upregulated in tumor displayed significant enrichments for lncRNAs as annotated in Gencode v12, for small RNAs, and for loci of conserved secondary structures (SISSIz ).Within the tumor samples, DE-probes upregulated in Basal-like tumors showed significant enrichment for known lncRNAs (Gencode v12, lncRNAdb ), for non-coding RNAs transcribed from introns , a […]


Widespread purifying selection on RNA structure in mammals

Nucleic Acids Res
PMCID: 3783177
PMID: 23847102
DOI: 10.1093/nar/gkt596

[…] riginal benchmarking pipeline that reproduces the experimental conditions of genome-wide sliding window methodologies, we improve the confidence and resolution of consensus-based ECS predictions with SISSIz and RNAz by creating tailor-made data sets of known structured RNAs and negative controls. Optimal prediction parameters are then extended to a high-throughput genomic screen via a massively pa […]


Examples of sequence conservation analyses capture a subset of mouse long non coding RNAs sharing homology with fish conserved genomic elements

BMC Bioinformatics
PMCID: 3633045
PMID: 23815359
DOI: 10.1186/1471-2105-14-S7-S14

[…] produced curves sensibly skewed below the diagonal line. Each alignment produced from the BLASTn search of the CNS dataset against zebrafish was also considered for structural conservation analysis. SISSIz program [] was used to randomize each alignment 100 times using a dinucleotide model (SISSIz --simulate --tstv -n 100) to generate a randomized alignment dataset to measure the structural conse […]


Pregnancy Induced Noncoding RNA (PINC) Associates with Polycomb Repressive Complex 2 and Regulates Mammary Epithelial Differentiation

PLoS Genet
PMCID: 3406180
PMID: 22911650
DOI: 10.1371/journal.pgen.1002840

[…] mPINC contained any structures that may interact with PRC2, we used the RNAstructure software to predict the secondary structure interactions of the mPINC isoforms mPINC1.0, mPINC1.6 and DRC2. Using SISSIz , we also looked for regions within the mPINC locus that showed significant evolutionary conservation of RNA secondary structure in all vertebrates (). As a result, we found two double hairpin […]

Want to access the full list of citations?

SISSIz reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SISSIz