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SISSIz specifications

Information


Unique identifier OMICS_14952
Name SISSIz
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

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Documentation


Maintainer


  • person_outline Stefan Washietl

Publication for SISSIz

SISSIz citations

 (11)
library_books

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

2016
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 […]

library_books

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

2015
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 […]

library_books

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

2014
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 […]

library_books

Widespread purifying selection on RNA structure in mammals

2013
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 […]

library_books

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

2013
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 […]

library_books

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

2012
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 […]


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