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sequence-shape specifications

Information


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
Requirements
Numpy, Scipy, Sklearn
Maintained Yes

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Versioning


No version available

Maintainers


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

Publication for sequence-shape

sequence-shape citations

 (4)
call_split

TMV mutants with poly(A) tracts of different lengths demonstrate structural variations in 3′UTR affecting viral RNAs accumulation and symptom expression

2015
Sci Rep
PMCID: 4683447
PMID: 26678425
DOI: 10.1038/srep18412
call_split See protocol

[…] ation. 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. […]

library_books

Full length RNA structure prediction of the HIV 1 genome reveals a conserved core domain

2015
Nucleic Acids Res
PMCID: 4666355
PMID: 26476446
DOI: 10.1093/nar/gkv1039

[…] ic 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 of […]

library_books

Structure Based Alignment and Consensus Secondary Structures for Three HIV Related RNA Genomes

2015
PLoS Comput Biol
PMCID: 4439019
PMID: 25992893
DOI: 10.1371/journal.pcbi.1004230

[…] ANL 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 between the SHAPE-struc […]

library_books

Acceleration of an Aromatic Claisen Rearrangement via a Designed Spiroligozyme Catalyst that Mimics the Ketosteroid Isomerase Catalytic Dyad

2014
J Am Chem Soc
PMCID: 4004270
PMID: 24456160
DOI: 10.1021/ja409214c

[…] pure, cyclic, functionalized bis-amino acids through pairs of amide bonds to create rigidified scaffolds that present functional groups in controlled three-dimensional constellations by virtue of the sequence, shape, and stereochemistry inherent in each chiral building block.− Previously, spiroligomers have been utilized as catalysts for the aldol reaction and transesterification reaction., We now […]

Citations

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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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