Alignment of NCBI Human Genome Resources Sequence Using High-Efficiency Low-Memory DIAMOND Sequence Aligner

The speed, sensitivity and quality of alignment of genomic sequences, either as comparative genomics or functional genomics, against a protein reference database is one of the most challenging computational tasks in bioinformatics field of study. Although recent methods offer improved performance over the well-known standard BLASTX, they exhibit only a modest speedup or low sensitivity. DIAMOND, with intensive attention to modern high-speed, high-performance, high-capacity computer architectures and the cache hierarchy, is a super-speed low memory sequence aligner for protein and translated DNA based on double indexing that searches and functions as a dropin replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.

Keywords:

Alignment , Bioinformatics , DIAMOND , Protein database , Sequence