{"id":"https://openalex.org/W2113289238","doi":"https://doi.org/10.1186/1751-0473-2-5","title":"OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences","display_name":"OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences","publication_year":2007,"publication_date":"2007-09-18","ids":{"openalex":"https://openalex.org/W2113289238","doi":"https://doi.org/10.1186/1751-0473-2-5","mag":"2113289238","pmid":"https://pubmed.ncbi.nlm.nih.gov/17877817"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-2-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-5","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-5","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100691558","display_name":"Guozhen Liu","orcid":"https://orcid.org/0000-0002-0556-6404"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guozhen Liu","raw_affiliation_strings":["Center for Molecular Medicine & Genetics, Wayne State University School of Medicine Detroit, MI 48201, USA. dwildman@med.wayne.edu","Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine Detroit, MI 48201, USA. dwildman@med.wayne.edu","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026464787","display_name":"Monica Uddin","orcid":"https://orcid.org/0000-0001-7404-2068"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Monica Uddin","raw_affiliation_strings":["Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081949447","display_name":"Munirul Islam","orcid":null},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Munirul Islam","raw_affiliation_strings":["Department of Computer Science, Wayne State University, Detroit, MI, 48201, USA","Department of Computer Science, Wayne State University, Detroit, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Department of Computer Science, Wayne State University, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112713998","display_name":"Morris Goodman","orcid":null},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Morris Goodman","raw_affiliation_strings":["Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","Department of Anatomy & Cell Biology, Wayne State University School of Medicine, Detroit, MI, 48201, USA","Department of Anatomy & Cell Biology, Wayne State University School of Medicine, Detroit, USA","Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Department of Anatomy & Cell Biology, Wayne State University School of Medicine, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Department of Anatomy & Cell Biology, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026416444","display_name":"Lawrence I. Grossman","orcid":"https://orcid.org/0000-0002-1059-9358"},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lawrence I Grossman","raw_affiliation_strings":["Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067511554","display_name":"Roberto Romero","orcid":"https://orcid.org/0000-0002-4448-5121"},"institutions":[{"id":"https://openalex.org/I1299022934","display_name":"United States Department of Health and Human Services","ror":"https://ror.org/033jnv181","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I4210144228","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210144228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roberto Romero","raw_affiliation_strings":["Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, 20892, USA","Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, USA","Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, 20892, USA","institution_ids":["https://openalex.org/I1299022934"]},{"raw_affiliation_string":"Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, USA","institution_ids":["https://openalex.org/I1299022934","https://openalex.org/I4210144228"]},{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064052128","display_name":"Derek E. Wildman","orcid":"https://orcid.org/0000-0002-6374-5136"},"institutions":[{"id":"https://openalex.org/I1299022934","display_name":"United States Department of Health and Human Services","ror":"https://ror.org/033jnv181","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934"]},{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]},{"id":"https://openalex.org/I4210144228","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210144228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek E Wildman","raw_affiliation_strings":["Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, 20892, USA","Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, 20892, USA","institution_ids":["https://openalex.org/I1299022934"]},{"raw_affiliation_string":"Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, USA","institution_ids":["https://openalex.org/I185443292"]},{"raw_affiliation_string":"Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, USA","institution_ids":["https://openalex.org/I1299022934","https://openalex.org/I4210144228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100691558"],"corresponding_institution_ids":["https://openalex.org/I185443292"],"apc_list":null,"apc_paid":null,"fwci":1.3454,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.79841323,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5343999862670898,"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":0.5343999862670898,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.3384999930858612,"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":0.05380000174045563,"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/refseq","display_name":"RefSeq","score":0.6943712830543518},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.6383090019226074},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.61822909116745},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5797117948532104},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5764332413673401},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5317555665969849},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5253700017929077},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5196470022201538},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4891670048236847},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4774087965488434},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.470402330160141},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.46847715973854065},{"id":"https://openalex.org/keywords/reading-frame","display_name":"Reading frame","score":0.42814725637435913},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4260566532611847},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.42403510212898254},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.42014554142951965},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10125651955604553}],"concepts":[{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.6943712830543518},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.6383090019226074},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.61822909116745},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5797117948532104},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5764332413673401},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5317555665969849},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5253700017929077},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5196470022201538},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4891670048236847},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4774087965488434},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.470402330160141},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.46847715973854065},{"id":"https://openalex.org/C166253671","wikidata":"https://www.wikidata.org/wiki/Q923372","display_name":"Reading frame","level":5,"score":0.42814725637435913},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4260566532611847},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.42403510212898254},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.42014554142951965},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10125651955604553}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1751-0473-2-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-5","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-5","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:17877817","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17877817","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:digitalcommons.wayne.edu:biomedcentral-1221","is_oa":false,"landing_page_url":"https://digitalcommons.wayne.edu/biomedcentral/159","pdf_url":null,"source":{"id":"https://openalex.org/S4377196394","display_name":"DigitalCommons - WayneState (Wayne State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I185443292","host_organization_name":"Wayne State University","host_organization_lineage":["https://openalex.org/I185443292"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Wayne State University Associated BioMed Central Scholarship","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:df3e14b6512c4a15b59174afb44f3639","is_oa":false,"landing_page_url":"https://doaj.org/article/df3e14b6512c4a15b59174afb44f3639","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code for Biology and Medicine, Vol 2, Iss 1, p 5 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2093931","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2093931","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-2-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-2-5","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-2-5","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337364","display_name":"National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113289238.pdf","grobid_xml":"https://content.openalex.org/works/W2113289238.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1522592213","https://openalex.org/W1689369637","https://openalex.org/W1981275193","https://openalex.org/W2067678211","https://openalex.org/W2072603644","https://openalex.org/W2097040991","https://openalex.org/W2106882534","https://openalex.org/W2112132489","https://openalex.org/W2114611642","https://openalex.org/W2119632499","https://openalex.org/W2122683221","https://openalex.org/W2125548284","https://openalex.org/W2144362290","https://openalex.org/W2146058063","https://openalex.org/W2151464048","https://openalex.org/W2152869198","https://openalex.org/W2164207497","https://openalex.org/W2165482734","https://openalex.org/W2168148721","https://openalex.org/W2168909179","https://openalex.org/W2171189056","https://openalex.org/W3217097258","https://openalex.org/W4285719527","https://openalex.org/W4292239814"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2133116680","https://openalex.org/W2730968108","https://openalex.org/W4386770652","https://openalex.org/W1482324242","https://openalex.org/W1886146948","https://openalex.org/W187239587","https://openalex.org/W2158700816","https://openalex.org/W2091678889","https://openalex.org/W2122131968"],"abstract_inverted_index":{"BACKGROUND:":[0],"Rapidly":[1],"accumulating":[2],"genome":[3],"sequence":[4,17,49,100],"data":[5],"from":[6,103,118,132,237],"multiple":[7,47,99],"species":[8,255],"offer":[9],"powerful":[10],"opportunities":[11],"for":[12,25,57,207],"the":[13,29,53,104,137,140,150,154,160,195,204,247],"detection":[14,220],"of":[15,60,107,110,120,165,171,211,221,246,277],"DNA":[16,48],"evolution.":[18],"Phylogenetic":[19],"tree":[20,217],"construction":[21],"and":[22,114,134,162,192,219,274,282],"codon-based":[23],"tests":[24],"natural":[26,222],"selection":[27],"are":[28,189,234,264],"prevailing":[30],"tools":[31],"used":[32],"to":[33,127,135,253],"detect":[34],"functionally":[35],"important":[36],"evolutionary":[37,83,182,273],"change":[38],"in":[39,70,144,175,260],"protein":[40,262],"coding":[41,105],"sequences.":[42,63],"These":[43],"analyses":[44,84,183,210,276],"often":[45,77],"require":[46],"alignments":[50,101,172,233],"that":[51,97,250,257],"maintain":[52],"correct":[54,196],"reading":[55,75,141,197],"frame":[56,142],"each":[58,166],"collection":[59],"putative":[61,116,129],"orthologous":[62,130],"Since":[64],"this":[65],"feature":[66],"is":[67,125,173],"not":[68],"available":[69,186],"most":[71,155],"alignment":[72,94,151,157],"tools,":[73],"codon":[74],"frames":[76],"must":[78],"be":[79],"checked":[80],"manually":[81],"before":[82],"can":[85,201],"commence.":[86],"RESULTS:":[87],"Here":[88],"we":[89],"report":[90],"an":[91],"online":[92],"codon-preserved":[93],"tool":[95,200],"(OCPAT)":[96],"generates":[98],"automatically":[102],"sequences":[106,214],"any":[108],"list":[109],"human":[111,227],"gene":[112,213],"IDs":[113],"their":[115],"orthologs":[117,138],"genomes":[119,133],"other":[121],"vertebrate":[122],"tetrapods.":[123],"OCPAT":[124,147,269],"programmed":[126],"extract":[128],"genes":[131,258],"align":[136],"with":[139],"maintained":[143],"all":[145,254],"species.":[146],"also":[148],"optimizes":[149],"by":[152,184],"trimming":[153],"variable":[156],"regions":[158],"at":[159,238],"5'":[161],"3'":[163],"ends":[164],"gene.":[167],"The":[168,199,268],"resulting":[169],"output":[170],"returned":[174],"several":[176],"formats,":[177],"which":[178],"facilitates":[179,271],"further":[180],"molecular":[181],"appropriate":[185],"software.":[187],"Alignments":[188],"generally":[190],"robust":[191],"reliable,":[193],"retaining":[194],"frame.":[198],"serve":[202],"as":[203],"first":[205],"step":[206],"comparative":[208],"genomic":[209],"protein-coding":[212],"including":[215],"phylogenetic":[216,275],"reconstruction":[218],"selection.":[223],"We":[224],"aligned":[225],"20,658":[226],"RefSeq":[228],"mRNAs":[229],"using":[230],"OCPAT.":[231],"Most":[232],"missing":[235],"sequence(s)":[236],"least":[239],"one":[240],"species;":[241],"however,":[242],"functional":[243],"annotation":[244],"clustering":[245],"~1700":[248],"transcripts":[249],"were":[251],"alignable":[252],"shows":[256],"involved":[259],"multi-subunit":[261],"complexes":[263],"highly":[265],"conserved.":[266],"CONCLUSION:":[267],"program":[270],"large-scale":[272],"entire":[278],"biological":[279],"processes,":[280],"pathways,":[281],"diseases.":[283]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
