CompleteCompositionVectorCLI 2.2.1 Build 6

Company: CompleteCompositionVectorCLI Team

Date Added: August 08, 2013 | Visits: 202

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The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, such methods are suboptimal for a rapidly growing dataset, because they require significant human effort, and because they increase in computational complexity quickly with the number of sequences. This project uses a method for genotyping that does not depend on multiple sequence alignment. It uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods.

Requirements: No special requirements

Platforms: Mac, Mac OSX

Keyword: Algorithm, Complete, Composition, Constituent, Derived, Kmers, Number, Represent, Sequences, Vector

Users rating: 0/10

License: Shareware

Size: 25.45 MB

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