CUDA-Sankoff-Web: A web tool to calculate the optimal secondary structural alignment

• Rodrigo Rocha Gomes IFB
• Daniel Sundfeld IFB

DOI: https://doi.org/10.5753/eradsp.2021.16697

Abstract

The sequence alignment is one of the most important operations in Bioinformatics. When considering RNA sequences, it is not enough to consider only the sequence itself, but the structures formed by them should also be considered. The optimal alignment of sequences has high computational complexity and can take a long time. Recently, CUDA-Sankoff was proposed to obtain the optimal secondary alignment of RNA sequences in a reasonable time using graphic processing units (GPUs). However, this tool does not have a friendly interface. In this work, we propose to create a web server that provides a graphical interface and helps the execution of the CUDA-Sankoff tool.

Keywords: Dedicated and specific architectures (GPUs, FPGAs, and others), High-Performance Computing

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