{"doi":"10.1145/3445967","title":"Data Structures to Represent a Set of <i>k</i> -long DNA Sequences","abstract":"The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k -mers, which are short fixed-length strings present in a dataset. While these approaches are rather diverse, storing and querying a k -mer set has emerged as a shared underlying component. A set of k -mers has unique features and applications that, over the past 10 years, have resulted in many specialized approaches for its representation. In this survey, we give a unified presentation and comparison of the data structures that have been proposed to store and query a k -mer set. We hope this survey will serve as a resource for researchers in the field as well as make the area more accessible to researchers outside the field.","journal":"ACM Computing Surveys","year":2021,"id":163276,"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":42,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.7843,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":682230,"name":"Jan Holub","orcid":"0000-0003-3022-2694","position":1,"is_corresponding":false},{"id":53921,"name":"Paul Medvedev","orcid":"0000-0003-3143-594X","position":2,"is_corresponding":false},{"id":550281,"name":"Rayan Chikhi","orcid":"0000-0003-1099-8735","position":0,"is_corresponding":true}],"reference_count":81,"raw_metadata":null,"created_at":"2026-07-18T23:45:17.971865Z","pmid":"41798316","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":[]}