Cytognomix Shannon Pipeline Client
This plugin allows you to run the Shannon Human Splicing Pipeline on a CLC Genomics Server. It can not be used to perform the analysis locally in the CLC Genomics Workbench. If you need this functionality please download the commercial plugin called "Cytognomix Shannon Pipeline".
The splicing mutation pipeline plug-in finds and interprets genomic variants that alter mRNA splicing in human exome, targeted sequencing, or complete genome data. Mutations that weaken or abolish natural splicing or activate cryptic splice sites are identified using our proven information theory-based methods.
Cytognomix genome-scale human splicing mutation analysis.
Cytognomix's Shannon pipeline was initially created to address the vexing problem of assessing the many variants of unknown significance that are detected in cancer genetic testing. The Shannon human splicing mutation plug-in uses a proven approach to predict mRNA splicing abnormalities based on single nucleotide variant data from human sequencing. The Cytognomix plug-in can be deployed on the CLC Genomics workbench either as a standalone application or to the CLC Genomics server using the Genomics Workbench client.
The Cytognomix Shannon plug-in identifies splicing mutations with industry-leading sensitivity and specificity. It is based on a legacy of peer-reviewed literature confirming validated mutation predictions using our patented information theory based technology. Changes in information content in splice sites correspond to actual differences in binding affinity. Input can either be CLC Bio SNP objects, in standard VCF, or an indexed simple SNP format. Results are based on sensible default parameters, are sortable and intuitive, and exportable to spreadsheets or genome browsers.
Mucaki et al. 2012 The Shannon pipeline has been used to reanalyze the Breast Cancer Information Core identifying many splicing mutations, most of which were previously unrecognized (Mucaki et al. 2012 ). Watch Dr. Peter Rogan at BioIT World explain how the CLC Bio version of the pipeline identified likely splicing mutations in the fully sequenced genomes of three common cancer cell lines.
Versioning and Requirements
The Cytognomix Shannon human mRNA splicing plug-in runs in standalone mode on the CLC Genomics Workbench V5.5 or with both the Workbench and CLC Genomics Server V.4.5 (as a standalone server or running Gridworks). Released for Linux and MacOSX Operating systems supporting Perl and gcc. Installation has been verified with Perl v.5.8.8 and 5.10.1 and gcc v.4.1.2 and v.4.4.3 with the Ubuntu 2.6.32-27 (32 and 64 bit), CentOS 2.6.18-238 (64 bit), and Fedora 16 (32 bit) kernels, and MacOSX (Lion release version 10.7.4; gcc v.4.2.1 and Perl 5.12.3) on hardware equipped with an Intel I7 processor and at least 4Gb RAM.
Trialing the Shannon Pipeline for mRNA Splicing Mutation Analysis
Experience the superior sensitivity and speed of the pipeline for yourself. After downloading the free client, you can connect to a trial version of Cytognomix’s commercial plugin installed on the CLC bio Genomics Server. There, you may work with the results of our genome-wide analysis of three different cancer cell lines (described in our upcoming paper1), or import your own variants and analyze them. Download Trial Shannon Pipeline Installation Guide for further details on the capabilities of the trial version and on how you may access it.
1Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences, Shirley BC, EJ Mucaki, T Whitehead, PI Costea, P Akan, and PK Rogan, Genomics, Proteomics, and Bioinformatics, in press.
- Hones in on a limited number of variants that potentially affect mRNA splicing
- Variants categorized by whether they fully or partially inactivate natural splice sites or activate cryptic sites
- Predicts variants missed by other bioinformatic methods
- Changes displayed graphically as Manhattan-like plots or custom tracks
- Mutations are sortable according to information content, proximity to natural splice site, relative strength of cryptic vs natural site, gene, and coordinate
- Variants affecting SNPs are annotated and can be filtered by allele frequency
- Rapid results generated from complete genome-wide, variant analysis of thousands of SNPs
- Variant tracks can be used as input for the Shannon Pipeline
Performance of Shannon pipeline plug-in on complete genome sequence data:
|Number of variants||Complete analysis time|
|211,049||1h 12 m|
|290,589||1h 22 m|
|314,637||1h 27 m|
The pipeline analyzes an average of 3198 variants/min on an I7-based server.