PLAST
PLAST – Local Alignment Search in Pangenome Graphs
PLAST is a freely available command-line tool for fast heuristic local alignment search in graphical pangenomes. It identifies high-scoring local alignments between nucleotide query sequences and pangenome graphs that can represent thousands of individual genomes. Input pangenomes can be provided as existing sequence graphs or generated from FASTA or FASTQ files containing complete genomes, assembled contigs, or raw sequencing reads.
Key benefits
Performs fast local alignment search in graphical pangenomes
Supports nucleotide queries against pangenome graphs representing many genomes
Accepts existing sequence graphs or FASTA/FASTQ-based genome collections
Uses a seed-and-extend approach for heuristic sequence alignment
Can enrich matches with information about contributing individual genomes
Applications
Graph-based pangenome analysis
Nucleotide sequence search across large genome collections
Comparative analysis of complete genomes, contigs, or raw reads
Identification of local sequence matches in pangenome contexts
Region- or subset-restricted searches based on genome presence or abundance
Intended use
PLAST is intended for bioinformaticians, comparative genomics researchers, microbial genomicists, pangenome researchers, and evolutionary biologists who need fast local sequence search in graph-based pangenome representations. It is particularly suited for users working with large genome collections who want to search nucleotide sequences in a pangenome-aware way and connect alignment results to the genomes contributing each match.
Contact:
Website