An automated signal alignment algorithm based on dynamic time warping for capillary electrophoresis data

Fethullah KARABİBER

Makale detayları

An automated signal alignment algorithm based on dynamic time warping for capillary electrophoresis data

Yazarlar:

Fethullah KARABİBER

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Electrical Engineering and Computer Science 2013 Vol.21 Issue 3, pp.851-863

Belge Tipi:

Makale

Yayın Tarihi:

2/2013

Belge Dili:

Türkçe

Document ID (Org No.):

2000743319

Sıklık:

İki Aylık

eISSN:

1303-6203

pISSN:

1300-0632

Özet:

 

Correcting the retention time variation and measuring the  similarity of time series is one of the most popular challenges in the  area of analyzing capillary electrophoresis (CE) data.  In this study,  an automated signal alignment method is proposed by modifying the  dynamic time warping (DTW) approach to align the time-series data.  Preprocessing tools and further optimizations were developed to  increase the performance of the algorithm.  As a demonstrative case  study, the developed algorithm is applied to the analysis of CE data  from a selective 2'-hydroxyl acylation analyzed by primer extension  (SHAPE) evaluation of the RNA secondary structure.  The time-shift  problem is one of the main components in the analysis of the SHAPE  data.  The accuracy and execution time of the algorithm are  illustrated with experimental results obtained by applying to  different types of data.  The experimental results show that the  signal alignment algorithm efficiently corrects the retention time  variation.  The developed tools can be readily adapted for the  analysis of other biological datasets or time series.

 

Correcting the retention time variation and measuring the  similarity of time series is one of the most popular challenges in the  area of analyzing capillary electrophoresis (CE) data.  In this study,  an automated signal alignment method is proposed by modifying the  dynamic time warping (DTW) approach to align the time-series data.  Preprocessing tools and further optimizations were developed to  increase the performance of the algorithm.  As a demonstrative case  study, the developed algorithm is applied to the analysis of CE data  from a selective 2'-hydroxyl acylation analyzed by primer extension  (SHAPE) evaluation of the RNA secondary structure.  The time-shift  problem is one of the main components in the analysis of the SHAPE  data.  The accuracy and execution time of the algorithm are  illustrated with experimental results obtained by applying to  different types of data.  The experimental results show that the  signal alignment algorithm efficiently corrects the retention time  variation.  The developed tools can be readily adapted for the  analysis of other biological datasets or time series.

Makale detayları

An automated signal alignment algorithm based on dynamic time warping for capillary electrophoresis data

Yazarlar: Fethullah KARABİBER

Yayıncı: TUBITAK

Dergi: Turkish Journal of Electrical Engineering and Computer Science 2013 Vol.21 Issue 3, pp.851-863

Belge Tipi: Makale

Yayın Tarihi: 2/2013

Belge Dili: Türkçe

Document ID (Org No.): 2000743319

Sıklık: İki Aylık

eISSN: 1303-6203

pISSN: 1300-0632

Sayı

Yazarlar:

Fethullah KARABİBER

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Electrical Engineering and Computer Science 2013 Vol.21 Issue 3, pp.851-863

Belge Tipi:

Makale

Yayın Tarihi:

2/2013

Belge Dili:

Türkçe

Document ID (Org No.):

2000743319

Sıklık:

İki Aylık

eISSN:

1303-6203

pISSN:

1300-0632