sequence-shape statistics

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sequence-shape specifications


Unique identifier OMICS_21634
Name sequence-shape
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Some DNA sequences.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Numpy, Scipy, Sklearn
Maintained Yes



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  • person_outline Remo Rohs <>
  • person_outline William Noble <>
  • person_outline Wenxiu Ma <>

Publication for sequence-shape

sequence-shape in publications

PMCID: 5870879
PMID: 28541376
DOI: 10.1093/bioinformatics/btx336

[…] k-mer kernel, for larger k; and (iii) the di-mismatch + shape kernel performs better than the di-mismatch kernel for intermediate k values., the software is available at, [email protected] or [email protected], are available at bioinformatics online., modeling transcription factor (tf) binding affinity and predicting tf binding sites […]

PMCID: 4683447
PMID: 26678425
DOI: 10.1038/srep18412

[…] the “force-read shape reactivity-pseudo energy constraints” option was chosen for the rna modeling under default setting of slope (kcal/mol) 1.8 and intercept (kcal/mol) −0.6 with the analyzed sequence shape file. the secondary structures and the corresponding shapes values were visualized using the varna java applet and further drew by graphic software., how to cite this article: guo, s. […]

PMCID: 4666355
PMID: 26476446
DOI: 10.1093/nar/gkv1039

[…] model that only uses information from shape data. we have previously shown that the performance of the ppfold 3.1 algorithm on large ribosomal data sets is comparable to rnastructure () for single-sequence shape-directed predictions, and superior in the case of moderately good alignments (). our structural model for the entire hiv-1 genome complements the watts09 model, and adds a new layer […]

PMCID: 4439019
PMID: 25992893
DOI: 10.1371/journal.pcbi.1004230

[…] alignments (sum-of-pairs and column scores report similarity to a reference alignment considering aligned position pairs and aligned columns, respectively). relative to lanl alignments, the three-sequence shape-dependent alignment considering hiv-1, sivcpz, and sivmac show sum-of-pairs and column scores of 75.5% and 56.9%, respectively. in general, areas of disagreement […]

PMCID: 4081404
PMID: 24991813
DOI: 10.1371/journal.pgen.1004457

[…] super-nucleosomal patterns. our results demonstrate that nucleosome-associated sequence periodicities are under selective pressure, implying that structural interactions between nucleosomes and dna sequence shape sequence evolution, particularly in introns., in eukaryotic cells, the majority of dna is packaged in nucleosomes comprised of ∼147 bp of dna wound tightly around the highly conserved […]

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sequence-shape institution(s)
Department of Statistics, University of California Riverside, Riverside, CA, USA; Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA, USA; Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
sequence-shape funding source(s)
Supported by National Institutes of Health award R01 GM106056 and by an Alfred P. Sloan Research Fellow.

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