{"id":"https://openalex.org/W2164786886","doi":"https://doi.org/10.1093/bioinformatics/btq665","title":"Mugsy: fast multiple alignment of closely related whole genomes","display_name":"Mugsy: fast multiple alignment of closely related whole genomes","publication_year":2010,"publication_date":"2010-12-09","ids":{"openalex":"https://openalex.org/W2164786886","doi":"https://doi.org/10.1093/bioinformatics/btq665","mag":"2164786886","pmid":"https://pubmed.ncbi.nlm.nih.gov/21148543"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq665","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq665","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/334/48864827/bioinformatics_27_3_334.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/334/48864827/bioinformatics_27_3_334.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010137910","display_name":"Samuel V. Angiuoli","orcid":"https://orcid.org/0000-0001-9525-4350"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samuel V. Angiuoli","raw_affiliation_strings":["1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park and 2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park and 2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010384159","display_name":"Steven L. Salzberg","orcid":"https://orcid.org/0000-0002-8859-7432"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]},{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven L. Salzberg","raw_affiliation_strings":["1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park and 2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA"],"affiliations":[{"raw_affiliation_string":"1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park and 2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010137910"],"corresponding_institution_ids":["https://openalex.org/I126744593","https://openalex.org/I66946132"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.0147,"has_fulltext":false,"cited_by_count":479,"citation_normalized_percentile":{"value":0.97863519,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"27","issue":"3","first_page":"334","last_page":"342"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.996999979019165,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/genome","display_name":"Genome","score":0.818997323513031},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5345126390457153},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5284340977668762},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.5098473429679871},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.5038277506828308},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4711519479751587},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.459811806678772},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44439828395843506},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.44227561354637146},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.434928834438324},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43442943692207336},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3401648998260498},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.324846088886261},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14554086327552795},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07887712121009827}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.818997323513031},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5345126390457153},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5284340977668762},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.5098473429679871},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.5038277506828308},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4711519479751587},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.459811806678772},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44439828395843506},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.44227561354637146},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.434928834438324},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43442943692207336},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3401648998260498},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.324846088886261},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14554086327552795},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07887712121009827},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013296","descriptor_name":"Streptococcus pneumoniae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013296","descriptor_name":"Streptococcus pneumoniae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013296","descriptor_name":"Streptococcus pneumoniae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013296","descriptor_name":"Streptococcus pneumoniae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq665","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq665","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/334/48864827/bioinformatics_27_3_334.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21148543","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21148543","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:pubmedcentral.nih.gov:3031037","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3031037","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq665","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq665","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/3/334/48864827/bioinformatics_27_3_334.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164786886.pdf","grobid_xml":"https://content.openalex.org/works/W2164786886.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1504417041","https://openalex.org/W1599305879","https://openalex.org/W1971926406","https://openalex.org/W1980397590","https://openalex.org/W1986009232","https://openalex.org/W1990061958","https://openalex.org/W1991330646","https://openalex.org/W2001725958","https://openalex.org/W2002531683","https://openalex.org/W2011289056","https://openalex.org/W2024975965","https://openalex.org/W2041257508","https://openalex.org/W2055615325","https://openalex.org/W2057998009","https://openalex.org/W2075996757","https://openalex.org/W2090044421","https://openalex.org/W2095581275","https://openalex.org/W2096525273","https://openalex.org/W2096771503","https://openalex.org/W2098816661","https://openalex.org/W2106882534","https://openalex.org/W2107248520","https://openalex.org/W2107282968","https://openalex.org/W2110291136","https://openalex.org/W2112132489","https://openalex.org/W2113213844","https://openalex.org/W2115313399","https://openalex.org/W2122598328","https://openalex.org/W2122732537","https://openalex.org/W2132926880","https://openalex.org/W2139317640","https://openalex.org/W2140698423","https://openalex.org/W2142642738","https://openalex.org/W2144362290","https://openalex.org/W2144767153","https://openalex.org/W2149342630","https://openalex.org/W2160379721","https://openalex.org/W2161546116","https://openalex.org/W2165686834","https://openalex.org/W2167673155","https://openalex.org/W2168909179","https://openalex.org/W2170702273","https://openalex.org/W2171547914","https://openalex.org/W2412439129","https://openalex.org/W2610179052","https://openalex.org/W4213060883","https://openalex.org/W4239678514","https://openalex.org/W6683215786","https://openalex.org/W6813364610"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W2949103014","https://openalex.org/W2155537421","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307"],"abstract_inverted_index":{"Mugsy":[0],"is":[1],"free,":[2],"open-source":[3],"software":[4],"available":[5],"from":[6],"http://mugsy.sf.net.":[7]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":39},{"year":2021,"cited_by_count":37},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":37},{"year":2018,"cited_by_count":46},{"year":2017,"cited_by_count":47},{"year":2016,"cited_by_count":45},{"year":2015,"cited_by_count":42},{"year":2014,"cited_by_count":49},{"year":2013,"cited_by_count":22},{"year":2012,"cited_by_count":19}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2025-10-10T00:00:00"}
