{"id":"https://openalex.org/W4224865640","doi":"https://doi.org/10.21105/joss.04296","title":"Pyrodigal: Python bindings and interface to Prodigal,an efficient method for gene prediction in prokaryotes","display_name":"Pyrodigal: Python bindings and interface to Prodigal,an efficient method for gene prediction in prokaryotes","publication_year":2022,"publication_date":"2022-04-25","ids":{"openalex":"https://openalex.org/W4224865640","doi":"https://doi.org/10.21105/joss.04296"},"language":"en","primary_location":{"id":"doi:10.21105/joss.04296","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.04296","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.04296.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.04296.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061398546","display_name":"Martin Larralde","orcid":"https://orcid.org/0000-0002-3947-4444"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Martin Larralde","raw_affiliation_strings":["Structural and Computational Biology Unit, EMBL, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Unit, EMBL, Heidelberg, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5061398546"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":7.1199,"has_fulltext":true,"cited_by_count":96,"citation_normalized_percentile":{"value":0.98162948,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"7","issue":"72","first_page":"4296","last_page":"4296"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9919999837875366,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.986299991607666,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9152315855026245},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6392156481742859},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.49942612648010254},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4801580309867859},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.45141837000846863},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2977915406227112},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2824394702911377}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9152315855026245},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6392156481742859},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.49942612648010254},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4801580309867859},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.45141837000846863},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2977915406227112},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2824394702911377},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.04296","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.04296","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.04296.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.04296","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.04296","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.04296.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2387072340","display_name":null,"funder_award_id":"SFB 1371","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7884568591","display_name":null,"funder_award_id":"SFB 137","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8235906861","display_name":null,"funder_award_id":"395357507","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4224865640.pdf","grobid_xml":"https://content.openalex.org/works/W4224865640.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2143485490","https://openalex.org/W2156858199","https://openalex.org/W2765745983","https://openalex.org/W2974075371","https://openalex.org/W2981913463","https://openalex.org/W3119160562","https://openalex.org/W3158368350","https://openalex.org/W3186058082"],"related_works":["https://openalex.org/W1906486629","https://openalex.org/W4318619745","https://openalex.org/W3021560500","https://openalex.org/W2166247150","https://openalex.org/W4243252198","https://openalex.org/W656686947","https://openalex.org/W3007645298","https://openalex.org/W2584070953","https://openalex.org/W3160881136","https://openalex.org/W1825954513"],"abstract_inverted_index":{"Larralde,":[0],"M.,":[1],"(2022).":[2],"Pyrodigal:":[3],"Python":[4],"bindings":[5],"and":[6],"interface":[7],"to":[8],"Prodigal,":[9],"an":[10],"efficient":[11],"method":[12],"for":[13],"gene":[14],"prediction":[15],"in":[16],"prokaryotes.":[17],"Journal":[18],"of":[19],"Open":[20],"Source":[21],"Software,":[22],"7(72),":[23],"4296,":[24],"https://doi.org/10.21105/joss.04296":[25]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":30},{"year":2023,"cited_by_count":8}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
