2024/03/01 by Hannes Hauswedell, Sara Hetzel, Simon Gene Gottlieb +3 · 1 voice · 2 citations
Biochemistry, Genetics and Molecular Biology · #Epigenetics and DNA Methylation #Genomics and Phylogenetic Studies #Genomics and Rare Diseases
paper · pdf · doi:10.1093/bioinformatics/btae097
openalex publication_date 2024/03/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
MOTIVATION: Local alignments of query sequences in large databases represent a core part of metagenomic studies and facilitate homology search. Following the development of NCBI Blast, many applications aimed to provide faster and equally sensitive local alignment frameworks. Most applications focus on protein alignments, while only few also facilitate DNA-based searches. None of the established programs allow searching DNA sequences from bisulfite sequencing experiments commonly used for DNA methylation profiling, for which specific alignment strategies need to be implemented. RESULTS: Here, we introduce Lambda3, a new version of the local alignment application Lambda. Lambda3 is the first solution that enables the search of protein, nucleotide as well as bisulfite-converted nucleotide query sequences. Its protein mode achieves comparable performance to that of the highly optimized protein alignment application Diamond, while the nucleotide mode consistently outperforms established local nucleotide aligners. Combined, Lambda3 presents a universal local alignment framework that enables fast and sensitive homology searches for a wide range of use-cases. AVAILABILITY AND IMPLEMENTATION: Lambda3 is free and open-source software publicly available at https://github.com/seqan/lambda/.