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J Comput Biol. 2015 Nov 30. [Epub ahead of print]

Metagenomic Classification Using an Abstraction Augmented Markov Model.

Author information

1
1 Sabre Corporation , Southlake, Texas.
2
2 Department of Statistical Science, Southern Methodist University , Dallas, Texas.

Abstract

The abstraction augmented Markov model (AAMM) is an extension of a Markov model that can be used for the analysis of genetic sequences. It is developed using the frequencies of all possible consecutive words with same length (p-mers). This article will review the theory behind AAMM and apply the theory behind AAMM in metagenomic classification.

KEYWORDS:

DNA sequencing; extensible Markov model; quasi-alignment; secondary structure

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