Dataset Information

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

ABSTRACT:

Summary

At the heart of many modern biotechnological and therapeutic applications lies the need to target specific genomic loci with pinpoint accuracy. Although landmark experiments demonstrate technological maturity in manufacturing and delivering genetic material, the genomic sequence analysis to find suitable targets lags behind. We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genomic architecture into account.

Availability

Source code and binaries are downloadable from www.bioinformatics.org.au/triplexator/inspector.

Contact

t.bailey@uq.edu.au

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Buske FA

PROVIDER: S-EPMC3712220 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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Publications

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Buske Fabian A FA Bauer Denis C DC Bauer Denis C DC Mattick John S JS Bailey Timothy L TL

Bioinformatics (Oxford, England) 20130605 15

<h4>Summary</h4>At the heart of many modern biotechnological and therapeutic applications lies the need to target specific genomic loci with pinpoint accuracy. Although landmark experiments demonstrate technological maturity in manufacturing and delivering genetic material, the genomic sequence analysis to find suitable targets lags behind. We provide a computational aid for the sophisticated design of sequence-specific ligands and selection of appropriate targets, taking gene location and genom ...[more]

PMID: 23740745

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Project description:BackgroundPrincipal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate workflows and analysis of molecular dynamics simulation data to fully harness the power of PCA is lacking. The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software.ResultsEmploying multi-threading, JEDi features a user-friendly interface to control rapid workflows for interrogating conformational motions of biopolymers at various spatial resolutions and within subregions, including multiple chain proteins. JEDi has options for Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) to construct covariance (Q), correlation (R), and partial correlation (P) matrices. Shrinkage and outlier thresholding are implemented for the accurate estimation of covariance. The effect of rare events is quantified using outlier and inlier filters. Applying sparsity thresholds in statistical models identifies latent correlated motions. Within a hierarchical approach, small-scale atomic motion is first calculated with a separate local cPCA calculation per residue to obtain eigenresidues. Then PCA on the eigenresidues yields rapid and accurate description of large-scale motions. Local cPCA on all residue pairs creates a map of all residue-residue dynamical couplings. Additionally, kernel PCA is implemented. JEDi output gives high quality PNG images by default, with options for text files that include aligned coordinates, several metrics that quantify mobility, PCA modes with their eigenvalues, and displacement vector projections onto the top principal modes. JEDi provides PyMol scripts together with PDB files to visualize individual cPCA modes and the essential dynamics occurring within user-selected time scales. Subspace comparisons performed on the most relevant eigenvectors using several statistical metrics quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes are available for both cPCA and dpPCA.ConclusionJEDi is a convenient toolkit that applies best practices in multivariate statistics for comparative studies on the essential dynamics of similar biopolymers. JEDi helps identify functional mechanisms through many integrated tools and visual aids for inspecting and quantifying similarity/differences in mobility and dynamic correlations.

Dataset Information

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Summary

Availability

Contact

Supplementary information

Publications

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Similar Datasets

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