Physical Sciences and Mathematics Commons^™

Highly Accurate And Sensitive Short Read Aligner, Mehmet Yağmur Gök, Sezer Gören Uğurdağ, Cem Ünsalan, Mahmut Şami̇l Sağiroğlu

Turkish Journal of Electrical Engineering and Computer Sciences

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 …