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Use ATCCfinder to identify commercially available American Type Culture Collection strains based on sequence queries
Samuel I Koehler1, Earl A Middlebrook1, Blake T Hovde1
1Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America.
Peerj
|August 18, 2025
Summary
Researchers can now easily find commercially available microbial strains and target genes using ATCCfinder software. This tool efficiently searches the American Type Culture Collection (ATCC) database for homologous sequences, simplifying strain identification and validation in microbiology research.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Historical microbiology research often used strains that are difficult to identify or validate due to limited sequencing resources.
- Identifying commercially available microbial strains or specific genes from sequence data is challenging, hindering research reproducibility and discovery.
- Public sequence databases contain variable quality data, making it difficult to reliably link sequences to specific, high-quality reference strains like those from the American Type Culture Collection (ATCC).
Purpose of the Study:
- To develop a software tool, ATCCfinder, for efficiently searching and identifying commercially available microbial strains and genetic components within the ATCC database.
- To overcome the limitations of existing methods for querying sequence similarity against curated ATCC reference genomes.
- To facilitate the validation of historical microbial strains and the discovery of strains with desired genetic elements from metagenomic studies.
Main Methods:
- ATCCfinder utilizes the ATCC application programming interface (API) to access and generate query-able databases from ATCC genome resources, including sequence, metadata, and annotation data.
- Nucleotide queries are compared against ATCC reference genomes using the minimap2 sequence alignment tool.
- Results are parsed and analyzed to provide summaries of homologous sequence matches to ATCC-available strains, with the capability to identify and download new ATCC references.
Main Results:
- ATCCfinder successfully generates query-able databases from ATCC sequence, metadata, and annotation data.
- The software efficiently identifies purchasable ATCC strains that are homologous to query sequences, including historical isolates, functional genes, and operons.
- ATCCfinder provides an updated target search database by identifying and downloading new ATCC references.
Conclusions:
- ATCCfinder offers an efficient solution for accessing, querying, and summarizing ATCC microbial resources.
- The software simplifies the identification of commercially available strains and genetic components, supporting microbiology research and strain validation.
- ATCCfinder enhances the ability to connect sequence data with specific, high-quality microbial reference strains available from ATCC.
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