TY - GEN
T1 - Array-based genome comparison of arabidopsis ecotypes using hidden markov models
AU - Seifert, Michael
AU - Banaei, Ali
AU - Keilwagen, Jens
AU - Mette, Michael Florian
AU - Houben, Andreas
AU - Roudier, François
AU - Colot, Vincent
AU - Grosse, Ivo
AU - Strickert, Marc
PY - 2009
Y1 - 2009
N2 - Arabidopsis thaliana is an important model organism in plant biology with a broad geographic distribution including ecotypes from Africa, America, Asia, and Europe. The natural variation of different ecotypes is expected to be reflected to a substantial degree in their genome sequences. Array comparative genomic hybridization (Array-CGH) can be used to quantify the natural variation of different ecotypes at the DNA level. Besides, such Array-CGH data provides the basics to establish a genome-wide map of DNA copy number variation for different ecotypes. Here, we present a new approach based on Hidden Markov Models (HMMs) to predict copy number variations in Array-CGH experiments. Using this approach, an improved genome-wide characterization of DNA segments with decreased or increased copy numbers is obtained in comparison to the routinely used segMNT algorithm. The software and the data set used in this case study can be downloaded from http://dig.ipk-gatersleben.de/HMMs/ACGH/ACGH.html.
AB - Arabidopsis thaliana is an important model organism in plant biology with a broad geographic distribution including ecotypes from Africa, America, Asia, and Europe. The natural variation of different ecotypes is expected to be reflected to a substantial degree in their genome sequences. Array comparative genomic hybridization (Array-CGH) can be used to quantify the natural variation of different ecotypes at the DNA level. Besides, such Array-CGH data provides the basics to establish a genome-wide map of DNA copy number variation for different ecotypes. Here, we present a new approach based on Hidden Markov Models (HMMs) to predict copy number variations in Array-CGH experiments. Using this approach, an improved genome-wide characterization of DNA segments with decreased or increased copy numbers is obtained in comparison to the routinely used segMNT algorithm. The software and the data set used in this case study can be downloaded from http://dig.ipk-gatersleben.de/HMMs/ACGH/ACGH.html.
KW - Arabidopsis Ecotypes
KW - Array-CGH
KW - Comparative Genomics
KW - Hidden Markov Model(HMM)
UR - http://www.scopus.com/inward/record.url?scp=67650519353&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:67650519353
SN - 9789898111654
T3 - BIOSIGNALS 2009 - Proceedings of the 2nd International Conference on Bio-Inspired Systems and Signal Processing
SP - 3
EP - 11
BT - BIOSIGNALS 2009 - Proceedings of the 2nd International Conference on Bio-Inspired Systems and Signal Processing
T2 - 2nd International Conference on Bio-Inspired Systems and Signal Processing, BIOSIGNALS 2009
Y2 - 14 January 2009 through 17 January 2009
ER -