TL;DR
MAFcounter is a new, efficient tool designed specifically for counting k-mers in MAF alignment files, addressing a gap in computational biology tools for analyzing sequence alignments.
Contribution
It introduces the first dedicated k-mer counting algorithm for MAF files, optimized for speed and memory efficiency, with multithreading support.
Findings
Fast and memory-efficient performance
Multithreaded processing capability
Open-source availability for broad use
Abstract
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity patterns, providing valuable insights into sequence conservation, evolutionary relationships and for functional analyses. Typically, sequence alignments are stored in formats such as the Multiple Alignment Format (MAF). Counting k-mer occurrences is a crucial task in many computational biology applications, but currently, there is no algorithm designed for k-mer counting in alignment files. Results: We have developed MAFcounter, the first k-mer counter dedicated to alignment files. MAFcounter is multithreaded, fast, and memory efficient, enabling k-mer counting in DNA and protein sequence alignment files. Availability: The MAFcounter package and…
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