{"doi":"10.1145/3584371.3612982","title":"On the Maximal Independent Sets of <i>k</i> -mers with the Edit Distance","abstract":"In computational biology, k-mers and edit distance are fundamental concepts. However, little is known about the metric space of all k-mers equipped with the edit distance. In this work, we explore the structure of the k-mer space by studying its maximal independent sets (MISs). An MIS is a sparse sketch of all k-mers with nice theoretical properties, and therefore admits critical applications in clustering, indexing, hashing, and sketching large-scale sequencing data, particularly those with high error-rates. Finding an MIS is a challenging problem, as the size of a k-mer space grows geometrically with respect to k. We propose three algorithms for this problem. The first and the most intuitive one uses a greedy strategy. The second method implements two techniques to avoid redundant comparisons by taking advantage of the locality-property of the k-mer space and the estimated bounds on the edit distance. The last algorithm avoids expensive calculations of the edit distance by translating the edit distance into the shortest path in a specifically designed graph. These algorithms are implemented and the calculated MISs of k-mer spaces and their statistical properties are reported and analyzed for k up to 15. Source code is freely available at https://github.com/Shao-Group/kmerspace.","journal":"PubMed","year":2023,"id":397429,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9406,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1173265,"name":"Ke Chen","orcid":"0000-0001-5470-6621","position":1,"is_corresponding":false},{"id":527409,"name":"Mingfu Shao","orcid":"0000-0001-6112-5139","position":2,"is_corresponding":false},{"id":1173264,"name":"Leran Ma","orcid":"0000-0001-5334-2061","position":0,"is_corresponding":true}],"reference_count":23,"raw_metadata":null,"created_at":"2026-07-19T01:19:39.497368Z","pmid":"38050580","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}