{"id":"https://openalex.org/W4414903669","doi":"https://doi.org/10.1093/bioinformatics/btaf558","title":"Parsing GTF and FASTA files using the eccLib Library","display_name":"Parsing GTF and FASTA files using the eccLib Library","publication_year":2025,"publication_date":"2025-10-01","ids":{"openalex":"https://openalex.org/W4414903669","doi":"https://doi.org/10.1093/bioinformatics/btaf558","pmid":"https://pubmed.ncbi.nlm.nih.gov/41056409"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf558","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf558","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf558","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5117343350","display_name":"Tomasz Chady","orcid":null},"institutions":[{"id":"https://openalex.org/I59411706","display_name":"Adam Mickiewicz University in Pozna\u0144","ror":"https://ror.org/04g6bbq64","country_code":"PL","type":"education","lineage":["https://openalex.org/I59411706"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Tomasz Chady","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, Adam Mickiewicz University Department of Mathematical Statistics and Data Analysis, , ul. Uniwersytetu Pozna\u0144skiego 4 , Pozna\u0144, 61-614,","Adam Mickiewicz University Faculty of Mathematics and Computer Science, , Pozna\u0144, 61-614,"],"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, Adam Mickiewicz University Department of Mathematical Statistics and Data Analysis, , ul. Uniwersytetu Pozna\u0144skiego 4 , Pozna\u0144, 61-614,","institution_ids":["https://openalex.org/I59411706"]},{"raw_affiliation_string":"Adam Mickiewicz University Faculty of Mathematics and Computer Science, , Pozna\u0144, 61-614,","institution_ids":["https://openalex.org/I59411706"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047395221","display_name":"Zuzanna Karolina Filutowska","orcid":"https://orcid.org/0000-0003-1815-7375"},"institutions":[{"id":"https://openalex.org/I59411706","display_name":"Adam Mickiewicz University in Pozna\u0144","ror":"https://ror.org/04g6bbq64","country_code":"PL","type":"education","lineage":["https://openalex.org/I59411706"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Zuzanna Karolina Filutowska","raw_affiliation_strings":["Faculty of Biology, Adam Mickiewicz University Department of Gene Expression, , ul. Uniwersytetu Pozna\u0144skiego 6 , Pozna\u0144, Wielkopolska, 61-614,","Adam Mickiewicz University Faculty of Biology, , Pozna\u0144, 61-614,"],"affiliations":[{"raw_affiliation_string":"Faculty of Biology, Adam Mickiewicz University Department of Gene Expression, , ul. Uniwersytetu Pozna\u0144skiego 6 , Pozna\u0144, Wielkopolska, 61-614,","institution_ids":["https://openalex.org/I59411706"]},{"raw_affiliation_string":"Adam Mickiewicz University Faculty of Biology, , Pozna\u0144, 61-614,","institution_ids":["https://openalex.org/I59411706"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5117343350"],"corresponding_institution_ids":["https://openalex.org/I59411706"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29645609,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13523","display_name":"Mathematics, Computing, and Information Processing","score":0.1906999945640564,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13523","display_name":"Mathematics, Computing, and Information Processing","score":0.1906999945640564,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8443999886512756},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.8073999881744385},{"id":"https://openalex.org/keywords/interpreter","display_name":"Interpreter","score":0.7310000061988831},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3587999939918518},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.3061000108718872}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8684999942779541},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8443999886512756},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8073999881744385},{"id":"https://openalex.org/C122783720","wikidata":"https://www.wikidata.org/wiki/Q183065","display_name":"Interpreter","level":2,"score":0.7310000061988831},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.7139000296592712},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4334999918937683},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4140999913215637},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3587999939918518},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.3061000108718872},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2558000087738037}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf558","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf558","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41056409","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41056409","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,"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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11359658","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12552103","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf558","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf558","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1978173716","https://openalex.org/W2753396470","https://openalex.org/W2964844385","https://openalex.org/W3035965352","https://openalex.org/W3117723450","https://openalex.org/W3131443014","https://openalex.org/W4405231264"],"related_works":[],"abstract_inverted_index":{"This":[0],"library":[1],"is":[2,13],"implemented":[3],"in":[4,45],"C":[5,28],"and":[6,36],"distributed":[7],"under":[8],"the":[9,20,34],"GPL-3.0":[10],"licence.":[11],"It":[12],"compatible":[14],"with":[15],"any":[16],"system":[17],"that":[18],"has":[19],"Python":[21],"interpreter":[22],"(CPython)":[23],"installed.":[24],"The":[25],"use":[26],"of":[27],"enables":[29],"numerous":[30],"optimizations":[31],"at":[32],"both":[33],"implementation":[35],"algorithmic":[37],"levels,":[38],"which":[39],"are":[40],"either":[41],"unachievable":[42],"or":[43],"impractical":[44],"Python.":[46]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}