Abstract
BackgroundPersonal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation. Though many methods have been developed, some are designed for small genome comparison while some are not efficient for large genome comparison. Moreover, most existing genome comparison tools have not been evaluated the correctness of sequence alignments systematically. A wrong sequence alignment would produce false sequence variants.ResultsIn this study, we present GSAlign that handles large genome sequence alignment efficiently and identifies sequence variants from the alignment result. GSAlign is an efficient sequence alignment tool for intra-species genomes. It identifies sequence variations from the sequence alignments. We estimate performance by measuring the correctness of predicted sequence variations. The experiment results demonstrated that GSAlign is not only faster than most existing state-of-the-art methods, but also identifies sequence variants with high accuracy.ConclusionsAs more genome sequences become available, the demand for genome comparison is increasing. Therefore an efficient and robust algorithm is most desirable. We believe GSAlign can be a useful tool. It exhibits the abilities of ultra-fast alignment as well as high accuracy and sensitivity for detecting sequence variations.
Highlights
Personal genomics and comparative genomics are becoming more important in clinical practice and genome research
It is foreseeable that genome sequencing will become a reality in clinical practices in the near future, which brings the study of personal genomics and comparative genomics
Though most of genome alignment tools do not output variants, we can identify variants by linearly scanning the sequence alignments. This measurement is sensitive to misalignments; we consider it is a fair measurement to estimate the performance of sequence alignment
Summary
Personal genomics and comparative genomics are becoming more important in clinical practice and genome research. Both fields require sequence alignment to discover sequence conservation and variation. Personal genomics involves the sequencing, analysis and interpretation of the genome of an individual. It can offer many clinical applications, in the diagnosis of genetic deficiencies and human diseases [2]. Comparative genomics is another field to study the genomic features of different organisms. It aims to understand the structure and function of genomes by
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