{"id":"https://openalex.org/W1834463255","doi":"https://doi.org/10.1002/0471250953.bi0405s01","title":"Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm","display_name":"Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm","publication_year":2003,"publication_date":"2003-03-01","ids":{"openalex":"https://openalex.org/W1834463255","doi":"https://doi.org/10.1002/0471250953.bi0405s01","mag":"1834463255","pmid":"https://pubmed.ncbi.nlm.nih.gov/18428700"},"language":"en","primary_location":{"id":"doi:10.1002/0471250953.bi0405s01","doi":"https://doi.org/10.1002/0471250953.bi0405s01","is_oa":false,"landing_page_url":"https://doi.org/10.1002/0471250953.bi0405s01","pdf_url":null,"source":{"id":"https://openalex.org/S4210177645","display_name":"Current Protocols in Bioinformatics","issn_l":"1934-3396","issn":["1934-3396","1934-340X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","norway-1","poland-140"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current Protocols in Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057317686","display_name":"Mark Yu. Borodovsky","orcid":"https://orcid.org/0000-0002-1401-4046","observed_orcids":["https://orcid.org/0000-0002-1401-4046"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Borodovsky","raw_affiliation_strings":["School of Biology and School of Biomedical Engineering, Georgia Institute of Technology Atlanta Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology and School of Biomedical Engineering, Georgia Institute of Technology Atlanta Georgia","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036795235","display_name":"Ryan E. Mills","orcid":"https://orcid.org/0000-0003-3425-6998","observed_orcids":["https://orcid.org/0000-0003-3425-6998"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Mills","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, Atlanta, Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, Atlanta, Georgia","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039539207","display_name":"John Besemer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Besemer","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, Atlanta, Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, Atlanta, Georgia","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083410058","display_name":"Alexandre Lomsadze","orcid":"https://orcid.org/0000-0003-0491-1648","observed_orcids":["https://orcid.org/0000-0003-0491-1648"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Lomsadze","raw_affiliation_strings":["School of Biology, Georgia Institute of Technology, Atlanta, Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Institute of Technology, Atlanta, Georgia","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":{"value":5050,"currency":"USD","value_usd":5050},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":105,"citation_normalized_percentile":{"value":0.07506624,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"1","issue":"1","first_page":"Unit4.5","last_page":"Unit4.5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genemark","display_name":"GeneMark","score":0.996999979019165},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.9509999752044678},{"id":"https://openalex.org/keywords/protein-coding-regions","display_name":"protein-coding regions","score":0.675000011920929},{"id":"https://openalex.org/keywords/whole-genome-analysis","display_name":"whole-genome analysis","score":0.6269999742507935},{"id":"https://openalex.org/keywords/genome-annotation","display_name":"genome annotation","score":0.5040000081062317}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.9300205111503601},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6100835204124451},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.6040741801261902},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5963314175605774},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5248087644577026},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4660813510417938},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4136129319667816},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4029233753681183},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3581925630569458},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3372310400009155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26546335220336914}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1002/0471250953.bi0405s01","doi":"https://doi.org/10.1002/0471250953.bi0405s01","is_oa":false,"landing_page_url":"https://doi.org/10.1002/0471250953.bi0405s01","pdf_url":null,"source":{"id":"https://openalex.org/S4210177645","display_name":"Current Protocols in Bioinformatics","issn_l":"1934-3396","issn":["1934-3396","1934-340X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","norway-1","poland-140"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current Protocols in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18428700","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18428700","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Current protocols in bioinformatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1652691445","https://openalex.org/W1971403296","https://openalex.org/W1986733193","https://openalex.org/W1998300401","https://openalex.org/W2009570821","https://openalex.org/W2039680623","https://openalex.org/W2041652393","https://openalex.org/W2057443273","https://openalex.org/W2075145136","https://openalex.org/W2106090237","https://openalex.org/W2110132014","https://openalex.org/W2128353077","https://openalex.org/W2143235667","https://openalex.org/W2152180708","https://openalex.org/W2160053034","https://openalex.org/W4239833500"],"related_works":["https://openalex.org/W2103919457","https://openalex.org/W1522333620","https://openalex.org/W2106090237","https://openalex.org/W2160053034","https://openalex.org/W2604046539","https://openalex.org/W2158808847","https://openalex.org/W2415288445","https://openalex.org/W7042584917","https://openalex.org/W1978164115","https://openalex.org/W7098567074"],"abstract_inverted_index":{"In":[0],"this":[1],"unit,":[2],"the":[3,15,35,55],"GeneMark":[4,23],"and":[5,42,63,66],"GeneMark.hmm":[6,46],"programs":[7],"are":[8],"presented":[9],"as":[10,31,33],"two":[11],"different":[12],"methods":[13,76],"for":[14,27,34,71,85],"in":[16,21,80],"silico":[17],"prediction":[18],"of":[19,38,49,89],"genes":[20],"prokaryotes.":[22],"can":[24,67,77],"be":[25,68,78],"used":[26,70,79],"whole":[28],"genome":[29,73],"analysis":[30,37],"well":[32],"local":[36],"a":[39,86],"particular":[40],"gene":[41,90],"its":[43],"surrounding":[44],"regions.":[45],"makes":[47],"use":[48],"Hidden":[50],"Markov":[51],"models":[52],"to":[53],"find":[54],"transition":[56],"points":[57],"(boundaries)":[58],"between":[59],"protein":[60],"coding":[61],"states":[62,65],"noncoding":[64],"efficiently":[69],"larger":[72],"sequences.":[74],"These":[75],"conjunction":[81],"with":[82],"each":[83],"other":[84],"higher":[87],"sensitivity":[88],"detection.":[91]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":9}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}