{"doi":"10.1093/bioinformatics/btaa633","title":"Machine Boss: rapid prototyping of bioinformatic automata","abstract":"MOTIVATION: Many software libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error-prone. RESULTS: We present Machine Boss, a software tool implementing not just inference and parameter-fitting algorithms, but also a set of operations for manipulating and combining automata. The aim is to make prototyping of bioinformatics HMMs as quick and easy as the construction of regular expressions, with one-line 'recipes' for many common applications. We report data from several illustrative examples involving protein-to-DNA alignment, DNA data storage and nanopore sequence analysis. AVAILABILITY AND IMPLEMENTATION: Machine Boss is released under the BSD-3 open source license and is available from http://machineboss.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2020,"id":115054,"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":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9579,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":539679,"name":"Yujie Wang","orcid":"0000-0001-5722-2673","position":1,"is_corresponding":false},{"id":539680,"name":"Mehak Sharma","orcid":"0000-0002-2134-5660","position":2,"is_corresponding":false},{"id":38015,"name":"Stephen Lin","orcid":"0000-0002-5616-558X","position":3,"is_corresponding":false},{"id":540611,"name":"Yolanda Shen","orcid":null,"position":4,"is_corresponding":false},{"id":539681,"name":"Shihab Dider","orcid":"0000-0001-9647-3643","position":5,"is_corresponding":false},{"id":382987,"name":"Ian Holmes","orcid":"0000-0001-7639-5369","position":6,"is_corresponding":false},{"id":539678,"name":"Jordi Silvestre-Ryan","orcid":"0000-0002-6520-5790","position":0,"is_corresponding":true}],"reference_count":48,"raw_metadata":null,"created_at":"2026-07-18T23:13:33.226937Z","pmid":"32683444","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":[]}