Lambda3

Lambda3 enables fast and sensitive local alignment and homology searches for protein, nucleotide, and bisulfite-converted nucleotide query sequences in large databases.

Key Features:

• Protein alignment mode: Achieves comparable performance to Diamond for protein alignment.
• Nucleotide alignment mode: Outperforms established local nucleotide aligners.
• Bisulfite-converted sequence search: Supports alignment of DNA sequences from bisulfite sequencing experiments used for DNA methylation profiling.
• Universal framework: Provides a single solution for protein, nucleotide, and bisulfite-converted nucleotide homology searches.

Scientific Applications:

• Metagenomic studies: Facilitates local alignments of query sequences in large databases for homology search.
• DNA methylation profiling: Enables searching of bisulfite-converted DNA sequences from bisulfite sequencing experiments.
• Protein homology search: Supports fast and sensitive protein sequence alignment against large databases.
• Nucleotide homology search: Supports DNA-based local alignment searches with improved performance over established aligners.

Methodology:

Lambda3 implements local alignment algorithms optimized for protein, nucleotide, and bisulfite-converted nucleotide sequences; specific alignment strategies are implemented for bisulfite-converted sequences to account for C-to-T conversions in DNA methylation profiling.