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#CompressGV

Citation | Abstract | Browser & HTTP Interface | Requirements | Installation

##Citation

Schlosberg A, Lam BYH, Yeo GSH, Clifton-Bligh RJ. DEFLATE Compression Algorithm Corrects for Overestimation of Phylogenetic Diversity by Grantham Approach to Single-Nucleotide Polymorphism Classification. International Journal of Molecular Sciences. 2014; 15(5):8491-8508.

Read online - Open Access

##Abstract

Background: Improvements in speed and cost of genome sequencing are resulting in increasing numbers of novel non-synonymous single nucleotide polymorphisms (nsSNPs) in genes known to be associated with disease. The large number of nsSNPs makes laboratory-based classification infeasible and familial co-segregation with disease is not always possible. In-silico methods for classification or triage are thus utilised. A popular tool based on multiple-species sequence alignments (MSAs), Align-GVGD, has been shown to underestimate deleterious effects, particularly as sequence numbers increase.

Results: We utilised the DEFLATE compression algorithm to account for expected variation across a number of species. With the adjusted Grantham measure we derived a means of quantitatively clustering known neutral and deleterious nsSNPs from the same gene; this was then used to assign novel variants to the most appropriate cluster as a means of binary classification. Scaling of clusters allows for inter-gene comparison of variants through a single pathogenecity score.

Conclusions: The approach improves upon the classification accuracy of Align-GVGD while correcting for sensitivity to large MSAs.

##Browser & HTTP Interface

A server running CompressGV is made available for anonymous usage; input data is destroyed immediately after classification and output is not stored. A browser-based interface is available for standard users. Low-volume usage directly over HTTP is encouraged for personal use only.

##Requirements

Versions in brackets refer to those used in development; earlier versions may be compatible but have not been tested.

• GNU Scientific Library + CBLAS (1.16)
• zlib (1.2.8)
• PSO implementation (kkentzo/pso 5a992b312e)

##Installation

A sample Linux makefile is included.

Copyright 2014 Arran Schlosberg.

This file is part of https://github.com/aschlosberg/CompressGV (CompressGV)

CompressGV is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

CompressGV is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with CompressGV. If not, see <http://www.gnu.org/licenses/>.