SaAlign: Multiple DNA/RNA sequence alignment and phylogenetic tree construction tool for ultra-large datasets and ultra-long sequences based on suffix array.

ABSTRACT: Multiple DNA/RNA sequence alignment is an important fundamental tool in bioinformatics, especially for phylogenetic tree construction. With DNA-sequencing improvements, the amount of bioinformatics data is constantly increasing, and various tools need to be iterated constantly. Mitochondrial genome analyses of multiple individuals and species require bioinformatics software; therefore, their performances need to be optimized. To improve the alignment of ultra-large datasets and ultra-long sequences, we optimized a dynamic programming algorithm using longest common substring methods. Ultra-large test DNA datasets, containing sequences of different lengths, some over 300 kb (kilobase), revealed that the Multiple DNA/RNA Sequence Alignment Tool Based on Suffix Tree (SaAlign) saved time and co

SUBMITTER: Wang Z 

PROVIDER: S-EPMC8976100 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature