SISSIz protocols

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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



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  • person_outline Stefan Washietl <>

Publication for SISSIz

SISSIz in pipelines

PMCID: 3783177
PMID: 23847102
DOI: 10.1093/nar/gkt596

[…] default scoring and ribosum scoring metric variants), using ‘rnadistance -dp’ from the vienna rna package version 1.8.5 ( (). the alignments are then scored with sissiz version 2.0 () (updated binaries can be downloaded from the supplementary information) using default parameters (‘-j’ option for ribosum scoring) and with rnaz version 2.0 () using […]

PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] the screens, e.g., by using di-nucleotide shuffling . a major challenge lies in providing good background models for shuffling multiple alignments. recent advances in that area include methods like sissiz and multiperm ., the multiperm program shuffles the multiple alignments, while preserving gap and local patterns of conservation, while also preserving the approximate di-nucleotide […]

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SISSIz in publications

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 […]

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

[…] taken into account. by convention, the reference sequence is always in the selected set otherwise the window is discarded. to provide random background for comparison the windows are shuffled with sissiz [], a tool which preserves relevant characteristics of the data, such as gap and local conservation patterns and the dinucleotide content. the original and the shuffled windows are screened […]

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

[…] 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 […]

PMCID: 3783177
PMID: 23847102
DOI: 10.1093/nar/gkt596

[…] pipeline aimed at calibrating the precision of genome-wide scans for consensus rna structure prediction. the benchmarking data obtained from two refined structure prediction algorithms, rnaz and sissiz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. when applied to consistency-based multiple genome alignments of 35 mammals, […]

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 […]

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