Shannon pipeline protocols

View Shannon pipeline computational protocol

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Shannon pipeline specifications

Information


Unique identifier OMICS_02631
Name Shannon pipeline
Interface Web user interface
Restrictions to use None
License Commercial
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publication for Shannon pipeline

Shannon pipeline in pipeline

2014
PMCID: 4231324
PMID: 25394353
DOI: 10.1038/srep07063

[…] reasons for our selection of strelka). protein coding mutations were annotated by annovar and splicing mutations with the shannon human splicing pipeline (, see for a list of all mutations). the shannon pipeline predicted significantly more splicing mutations than reported by tcga, because the information-theoretic method employed enables analyses of variants beyond exon boundaries […]


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Shannon pipeline in publications

 (2)
PMCID: 4828881
PMID: 27067391
DOI: 10.1186/s12920-016-0178-5

[…] information weight matrices (based on the method described by schneider et al. 1984; n = 147) (see additional file : methods) []. all utr variants were assessed using a modified version of the shannon pipeline [] containing the rbpdb and cisbp-rna models. results were filtered to include a) variants with |δri| ≥ 4.0 bits, b) variants creating or strengthening sites (ri,final ≥ rsequence […]

PMCID: 4231324
PMID: 25394353
DOI: 10.1038/srep07063

[…] was used with default parameters to predict which variants are likely to affect amino acid sequence and splicing at the natural splice sites. the shannon human splicing pipeline version 2.0 (shannon pipeline) was used to complete a more in-depth analysis of splicing mutations, which predicts variants that will alter the binding affinity of the natural site or cause cryptic splicing (i.e. […]


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Shannon pipeline institution(s)
Department of Computer Science, Middlesex College, The University of Western Ontario, London, ON, Canada

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