{"id":"https://openalex.org/W2077377665","doi":"https://doi.org/10.1093/nar/gkl069","title":"MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes","display_name":"MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2077377665","doi":"https://doi.org/10.1093/nar/gkl069","mag":"2077377665","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845027"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl069","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl069","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W366/7622699/gkl069.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W366/7622699/gkl069.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077099192","display_name":"Shane Neph","orcid":"https://orcid.org/0000-0003-2962-8777"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S. Neph","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350, USA","Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA, 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA, 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008676408","display_name":"Martin Tompa","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Tompa","raw_affiliation_strings":["Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington Box 352350, Seattle, WA 98195-2350, USA","Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington  Box 352350, Seattle, WA 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington Box 352350, Seattle, WA 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington  Box 352350, Seattle, WA 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077099192"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.7728,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.83424351,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"34","issue":"Web Server","first_page":"W366","last_page":"W368"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8956928253173828},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7906275391578674},{"id":"https://openalex.org/keywords/footprinting","display_name":"Footprinting","score":0.7441704273223877},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6664198040962219},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5608458518981934},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5049598813056946},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.47523167729377747},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4669896960258484},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44460529088974},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.42332717776298523},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.4122849702835083},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3548375368118286},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25953102111816406},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.13831079006195068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.08211645483970642}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8956928253173828},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7906275391578674},{"id":"https://openalex.org/C2778021871","wikidata":"https://www.wikidata.org/wiki/Q648006","display_name":"Footprinting","level":4,"score":0.7441704273223877},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6664198040962219},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5608458518981934},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5049598813056946},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.47523167729377747},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4669896960258484},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44460529088974},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.42332717776298523},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4122849702835083},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3548375368118286},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25953102111816406},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.13831079006195068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.08211645483970642},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkl069","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl069","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W366/7622699/gkl069.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845027","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.969.7169","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.969.7169","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/suppl_2/W366.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:1334003","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC1538893","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538893","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl069","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl069","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl069","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W366/7622699/gkl069.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1836573911","display_name":"ITR: Discovering Regulatory Elements in Biological Sequences","funder_award_id":"0218798","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/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2077377665.pdf","grobid_xml":"https://content.openalex.org/works/W2077377665.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1974614108","https://openalex.org/W1984053739","https://openalex.org/W2041726559","https://openalex.org/W2054624670","https://openalex.org/W2058682865","https://openalex.org/W2074530889","https://openalex.org/W2085442947","https://openalex.org/W2095724872","https://openalex.org/W2122679732","https://openalex.org/W2134591904","https://openalex.org/W2135221645","https://openalex.org/W2165380507","https://openalex.org/W4251391134"],"related_works":["https://openalex.org/W2739728095","https://openalex.org/W2065083790","https://openalex.org/W2103040549","https://openalex.org/W2604174992","https://openalex.org/W1522689712","https://openalex.org/W2057191541","https://openalex.org/W2105489997","https://openalex.org/W2159892619","https://openalex.org/W2386553998","https://openalex.org/W1988675506"],"abstract_inverted_index":{"Phylogenetic":[0],"footprinting":[1],"is":[2,71,75],"a":[3,12],"method":[4],"for":[5,46],"the":[6,28,55,59],"discovery":[7],"of":[8,14,54],"regulatory":[9,16],"elements":[10],"in":[11,32,49,62],"set":[13],"homologous":[15,34,60],"regions,":[17],"usually":[18],"collected":[19],"from":[20],"multiple":[21],"species.":[22],"It":[23],"does":[24],"so":[25],"by":[26],"identifying":[27],"most":[29],"conserved":[30],"motifs":[31],"those":[33],"regions.":[35],"This":[36],"note":[37],"describes":[38],"web":[39],"software":[40,70],"that":[41],"has":[42],"been":[43],"designed":[44],"specifically":[45],"this":[47],"purpose":[48],"prokaryotic":[50],"genomes,":[51],"making":[52],"use":[53],"phylogenetic":[56],"relationships":[57],"among":[58],"sequences":[61],"order":[63],"to":[64],"make":[65],"more":[66],"accurate":[67],"predictions.":[68],"The":[69],"called":[72],"MicroFootPrinter":[73],"and":[74],"available":[76],"at":[77],"http://bio.cs.washington.edu/software.html.":[78]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}