Title :
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies
Author :
Artyomenko, Alexander ; Mancuso, Nicholas ; Zelikovsky, Alex ; Skums, Pavel ; Mandoiu, Ion
Author_Institution :
Dept. of Comput. Sci., Georgia State Univ., Atlanta, GA, USA
Abstract :
The main challenge in local viral quasispecies reconstruction is to eliminate sequencing errors while preserving the natural heterogeneity of the viral population. This paper presents a new approach to error correction via an expectation maximization (EM) method.
Keywords :
expectation-maximisation algorithm; genomics; microorganisms; EM based algorithm; expectation maximization method; kGEM; sequencing errors; viral population natural heterogeneity; viral quasispecies local reconstruction; Computer science; Educational institutions; Error correction; Frequency estimation; Sensitivity; Sociology; Next-generation sequencing; error correction; expectation maximization; local reconstruction; viral quasispecies;
Conference_Titel :
Computational Advances in Bio and Medical Sciences (ICCABS), 2013 IEEE 3rd International Conference on
Conference_Location :
New Orleans, LA
DOI :
10.1109/ICCABS.2013.6629226
