{"doi":"10.1101/2020.02.13.945071","title":"Machine Boss: Rapid Prototyping of Bioinformatic Automata","abstract":"ABSTRACT Motivation Many C++ 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/ . Contact Ian Holmes, ihh@berkeley.edu","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":126272,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9517,"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":21173,"name":"Y. Wang","orcid":"0000-0003-4693-5365","position":1,"is_corresponding":false},{"id":574245,"name":"Madhvi Sharma","orcid":null,"position":2,"is_corresponding":false},{"id":573681,"name":"Simon Lin","orcid":"0000-0002-3003-3394","position":3,"is_corresponding":false},{"id":573682,"name":"Yulin Shen","orcid":"0000-0003-1635-6661","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":51,"raw_metadata":null,"created_at":"2026-07-18T23:15:23.509897Z","pmid":null,"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":[]}