Highly accurate and sensitive short read aligner

Mehmet Yağmur GÖK; Sezer Gören UĞURDAĞ; Cem ÜNSALAN; Mahmut Şamil SAĞIROĞLU

Makale detayları

Highly accurate and sensitive short read aligner

Yazarlar:

Mehmet Yağmur GÖK | Sezer Gören UĞURDAĞ | Cem ÜNSALAN | Mahmut Şamil SAĞIROĞLU

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Electrical Engineering and Computer Science 2018 Vol.26 Issue 2, pp.721-731

Belge Tipi:

Makale

Yayın Tarihi:

3/2018

Belge Dili:

Türkçe

Document ID (Org No.):

2000735226

Sıklık:

İki Aylık

eISSN:

1303-6203

pISSN:

1300-0632

Özet:

 

Next-generation sequencing generates large numbers of   short reads from DNA. This makes it difficult to process and store.   Therefore, efficient sequence alignment and mapping techniques are needed in   bioinformatics. Alignment and mapping are the basic steps involved in   genetic data analysis. The Smith-Waterman (SW) algorithm, a well-known   dynamic programming algorithm, is often used for this purpose. In this work,   we propose to utilize Phred quality scores in Gotoh's affine gap model to   increase the accuracy and sensitivity of the SW algorithm. Hardware   platforms such as FPGAs and GPUs are commonly used to solve computationally   expensive problems. In this work, a hybrid PC-FPGA system is built where the   SW algorithm based on the affine gap model with Phred quality scores is   implemented on the FPGA and a read compressor is implemented on the host PC.   We compare our method with state-of-the-art systems such as Bowtie, BWA, and   the Kim-Olson FPGA-based system in terms of sensitivity, accuracy, and   speed. Based on extensive experiments, we observed that our proposed method   is more sensitive and accurate as compared to other solutions.

Makale detayları

Highly accurate and sensitive short read aligner

Yazarlar: Mehmet Yağmur GÖK | Sezer Gören UĞURDAĞ | Cem ÜNSALAN | Mahmut Şamil SAĞIROĞLU

Yayıncı: TUBITAK

Dergi: Turkish Journal of Electrical Engineering and Computer Science 2018 Vol.26 Issue 2, pp.721-731

Belge Tipi: Makale

Yayın Tarihi: 3/2018

Belge Dili: Türkçe

Document ID (Org No.): 2000735226

Sıklık: İki Aylık

eISSN: 1303-6203

pISSN: 1300-0632

Sayı

Yazarlar:

Mehmet Yağmur GÖK | Sezer Gören UĞURDAĞ | Cem ÜNSALAN | Mahmut Şamil SAĞIROĞLU

Yayıncı:

TUBITAK

Dergi:

Turkish Journal of Electrical Engineering and Computer Science 2018 Vol.26 Issue 2, pp.721-731

Belge Tipi:

Makale

Yayın Tarihi:

3/2018

Belge Dili:

Türkçe

Document ID (Org No.):

2000735226

Sıklık:

İki Aylık

eISSN:

1303-6203

pISSN:

1300-0632