Abstract
The alignment of multiple protein or DNA sequences is a common task in many biological fields. These alignments may then be used to identify conserved regions or positions, which could in turn be used to score the likely pathogenicity of a sequence change in a patient, detect functional domains that can determine the activity of an unknown gene, or map evolutionary relationships by tracking changes in conserved regions. The development of high-throughput sequencing technologies has trivialised the generation of sequencing data, which is made available through public repositories, such as GenBank, hosted by the NCBI. In October 2024, GenBank held approximately 4.7 billion sequences from over 580,000 species. Consequently, the constraints of multiple sequence alignment estimation have moved from data generation to data retrieval, extraction and filtering. While human-curated datasets for widely used sequences have been released, retrieving datasets for less commonly used sequences can be onerous. Therefore, we have developed GeneMatrix, an application that aids the extraction, filtering, aggregation, and alignment of DNA and protein sequences from GenBank-formatted files of single gene sequences or genomes such as viruses and mitochondria.