Repository: Freie Universit├Ąt Berlin, Math Department

Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences

Hauswedell, Hannes and Hetzel, Sara and Gottlieb, Simon G and Kretzmer, Helene and Meissner, Alexander and Reinert, Knut and Cowen, Lenore (2024) Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics, 40 (3). ISSN 1367-4811

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Official URL: https://doi.org/10.1093/bioinformatics/btae097

Abstract

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/.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:3143
Deposited By: Anja Kasseckert
Deposited On:18 Apr 2024 11:00
Last Modified:18 Apr 2024 11:44

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