{"id":"https://openalex.org/W2155368965","doi":"https://doi.org/10.1093/bioinformatics/bts599","title":"Real Time Metagenomics: Using <i>k</i>-mers to annotate metagenomes","display_name":"Real Time Metagenomics: Using <i>k</i>-mers to annotate metagenomes","publication_year":2012,"publication_date":"2012-10-09","ids":{"openalex":"https://openalex.org/W2155368965","doi":"https://doi.org/10.1093/bioinformatics/bts599","mag":"2155368965","pmid":"https://pubmed.ncbi.nlm.nih.gov/23047562"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts599","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts599","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"green","oa_url":"https://www.osti.gov/servlets/purl/1625280","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036802114","display_name":"Robert A. Edwards","orcid":"https://orcid.org/0000-0001-8383-8949"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert A. Edwards","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015210172","display_name":"Robert Olson","orcid":"https://orcid.org/0000-0001-9751-4734"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Olson","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111684840","display_name":"Terry Disz","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Terry Disz","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066616906","display_name":"Gordon D. Pusch","orcid":"https://orcid.org/0000-0003-1471-0401"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gordon D. Pusch","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036781580","display_name":"Veronika Vonstein","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Veronika Vonstein","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053682943","display_name":"Rick Stevens","orcid":"https://orcid.org/0000-0002-4268-4020"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rick Stevens","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085138988","display_name":"Ross Overbeek","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ross Overbeek","raw_affiliation_strings":["1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, 2Department of Biology, 3Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, 4Computation Institute, University of Chicago, Chicago, IL 60637, USA and 5Fellowship for the Interpretation of Genomes, Burr Ridge, IL 60527, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.7808,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.91192442,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"24","first_page":"3316","last_page":"3317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9945999979972839,"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/perl","display_name":"Perl","score":0.8209062218666077},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7767100930213928},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7152360081672668},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6615310907363892},{"id":"https://openalex.org/keywords/file-transfer-protocol","display_name":"File Transfer Protocol","score":0.6174502372741699},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5590271949768066},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.5442663431167603},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.44216033816337585},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4415074586868286},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43513205647468567},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4230673909187317},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3678610920906067},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35471874475479126},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22107762098312378},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.21761050820350647},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21555611491203308},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12153446674346924},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09264630079269409}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.8209062218666077},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7767100930213928},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7152360081672668},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6615310907363892},{"id":"https://openalex.org/C169485995","wikidata":"https://www.wikidata.org/wiki/Q42283","display_name":"File Transfer Protocol","level":3,"score":0.6174502372741699},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5590271949768066},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.5442663431167603},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.44216033816337585},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4415074586868286},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43513205647468567},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4230673909187317},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3678610920906067},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35471874475479126},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22107762098312378},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.21761050820350647},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21555611491203308},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12153446674346924},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09264630079269409},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts599","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts599","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23047562","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23047562","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:osti.gov:1625280","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1625280","pdf_url":"https://www.osti.gov/servlets/purl/1625280","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:europepmc.org:2576864","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3519453","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":"pmh:oai:osti.gov:1625280","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1625280","pdf_url":"https://www.osti.gov/servlets/purl/1625280","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2237120788","display_name":"Dimensions: Shedding Light on Viral Dark Matter - Genetic, Taxonomic, and Functional Diversity of Coral Reef Viromes","funder_award_id":"1046413","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4038868185","display_name":null,"funder_award_id":"1046413","funder_id":"https://openalex.org/F4320337400","funder_display_name":"Division of Environmental Biology"},{"id":"https://openalex.org/G8278258816","display_name":"Collaborative Research:  PHANTOME:  PHage ANnotation TOols and MEthods","funder_award_id":"0850356","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"},{"id":"https://openalex.org/F4320337400","display_name":"Division of Environmental Biology","ror":"https://ror.org/03g87he71"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155368965.pdf"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1975970608","https://openalex.org/W1989348205","https://openalex.org/W2114034054","https://openalex.org/W2123009189","https://openalex.org/W2131342905","https://openalex.org/W2155545841","https://openalex.org/W2159406441","https://openalex.org/W2914037595","https://openalex.org/W4230758978","https://openalex.org/W6683179183"],"related_works":["https://openalex.org/W2480056510","https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2103737347","https://openalex.org/W2744807401","https://openalex.org/W1431931776","https://openalex.org/W2393167804"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"Annotation":[2],"of":[3,14,72,89],"metagenomes":[4,46],"involves":[5],"comparing":[6],"the":[7,68,87,90,117],"individual":[8],"sequence":[9],"reads":[10],"with":[11],"a":[12,19,27,41,107],"database":[13],"known":[15],"sequences":[16,51],"and":[17,66,70,93,102,127],"assigning":[18],"unique":[20,48],"function":[21],"to":[22,44,54,85,115],"each":[23],"read.":[24],"This":[25,95],"is":[26,31,120],"time-consuming":[28],"task":[29],"that":[30,61],"computationally":[32,36],"intensive":[33],"(though":[34],"not":[35],"complex).":[37],"Here":[38],"we":[39],"present":[40],"novel":[42],"approach":[43,67,81],"annotate":[45],"using":[47],"k-mer":[49],"oligopeptide":[50],"from":[52,124,133],"7":[53],"12":[55],"amino":[56],"acids":[57],"long.":[58],"We":[59],"demonstrate":[60],"k-mer-based":[62],"annotations":[63,74],"are":[64,129,141],"faster":[65],"sensitivity":[69],"precision":[71],"blastx-based":[73],"without":[75],"loosing":[76],"accuracy.":[77],"A":[78],"last-common":[79],"ancestor":[80],"was":[82,98],"also":[83],"developed":[84],"describe":[86],"members":[88],"community.":[91],"Availability":[92],"implementation:":[94],"open-source":[96],"application":[97],"implemented":[99],"in":[100],"Perl":[101],"can":[103],"be":[104],"accessed":[105],"via":[106],"user-friendly":[108],"website":[109],"at":[110,143],"http://edwards.sdsu.edu/rtmg.":[111],"In":[112],"addition,":[113],"code":[114],"access":[116],"annotation":[118],"servers":[119],"available":[121,130,142],"for":[122,131],"download":[123,132],"http://www.theseed.org/.":[125],"FIGfams":[126],"k-mers":[128],"ftp://ftp.theseed.org/FIGfams/.":[134],"Contact:":[135],"redwards@mail.sdsu.edu":[136],"Supplementary":[137,139],"information:":[138],"data":[140],"Bioinformatics":[144],"online.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}
