{"id":"https://openalex.org/W2164335278","doi":"https://doi.org/10.1186/1748-7188-5-24","title":"AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences","display_name":"AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences","publication_year":2010,"publication_date":"2010-06-02","ids":{"openalex":"https://openalex.org/W2164335278","doi":"https://doi.org/10.1186/1748-7188-5-24","mag":"2164335278","pmid":"https://pubmed.ncbi.nlm.nih.gov/20525162"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-5-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-24","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-24","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-24","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111478946","display_name":"Dar\u00edo Guerrero","orcid":null},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Dar\u00edo Guerrero","raw_affiliation_strings":["Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa, 34, 29590 M\u00e1laga, Spain. claros@uma.es","Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa 34, 29590, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa, 34, 29590 M\u00e1laga, Spain. claros@uma.es","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa 34, 29590, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074979435","display_name":"Roc\u00ed\u00ado Bautista","orcid":"https://orcid.org/0000-0003-1685-8119"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Roc\u00edo Bautista","raw_affiliation_strings":["Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa 34, 29590, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa 34, 29590, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108534734","display_name":"David P. Villalobos","orcid":null},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David P Villalobos","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica (Universidad de M\u00e1laga), Campus de Teatinos, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica (Universidad de M\u00e1laga), Campus de Teatinos, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026821618","display_name":"Francisco R. Cant\u00f3n","orcid":"https://orcid.org/0000-0001-6917-8630"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francisco R Cant\u00f3n","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica (Universidad de M\u00e1laga), Campus de Teatinos, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica (Universidad de M\u00e1laga), Campus de Teatinos, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056017872","display_name":"M. Gonzalo Claros","orcid":"https://orcid.org/0000-0002-0112-3550"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"M Gonzalo Claros","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica (Universidad de M\u00e1laga), Campus de Teatinos, 29071, M\u00e1laga, Spain","Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa 34, 29590, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica (Universidad de M\u00e1laga), Campus de Teatinos, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica (Universidad de M\u00e1laga), Severo Ochoa 34, 29590, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056017872"],"corresponding_institution_ids":["https://openalex.org/I82767444"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":0.3734,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.61125934,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"5","issue":"1","first_page":"24","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.22470000386238098,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.22470000386238098,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.08609999716281891,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.07000000029802322,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6476550102233887},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6349817514419556},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4718496799468994},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4053668975830078},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3215276002883911},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29050731658935547},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18305522203445435}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6476550102233887},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6349817514419556},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4718496799468994},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4053668975830078},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3215276002883911},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29050731658935547},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18305522203445435}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1748-7188-5-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-24","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-24","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:20525162","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20525162","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:cf7c0b43ec1c4949937b8dc6e99804f6","is_oa":false,"landing_page_url":"https://doaj.org/article/cf7c0b43ec1c4949937b8dc6e99804f6","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":"Algorithms for Molecular Biology, Vol 5, Iss 1, p 24 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2902484","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2902484","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-5-24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-24","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-24","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1320307708","display_name":null,"funder_award_id":"BIO2009-07490","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G7825495982","display_name":null,"funder_award_id":"PLE2009","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G862819838","display_name":null,"funder_award_id":"BIO-114","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G863065016","display_name":null,"funder_award_id":"BIO2009-07490","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164335278.pdf","grobid_xml":"https://content.openalex.org/works/W2164335278.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W77717277","https://openalex.org/W240655252","https://openalex.org/W1574123983","https://openalex.org/W1967293793","https://openalex.org/W1980037825","https://openalex.org/W1994421021","https://openalex.org/W1996281908","https://openalex.org/W2005903864","https://openalex.org/W2015292449","https://openalex.org/W2018009271","https://openalex.org/W2034767282","https://openalex.org/W2041877620","https://openalex.org/W2044586667","https://openalex.org/W2049349724","https://openalex.org/W2053618775","https://openalex.org/W2074231493","https://openalex.org/W2079166554","https://openalex.org/W2098640392","https://openalex.org/W2099983847","https://openalex.org/W2115427976","https://openalex.org/W2123376874","https://openalex.org/W2131463690","https://openalex.org/W2138369959","https://openalex.org/W2140031146","https://openalex.org/W2145044811","https://openalex.org/W2145191876","https://openalex.org/W2146931904","https://openalex.org/W2150934173","https://openalex.org/W2152688507","https://openalex.org/W2154960571","https://openalex.org/W2156256232","https://openalex.org/W2158715856","https://openalex.org/W2160477085","https://openalex.org/W2162238964","https://openalex.org/W2170831688","https://openalex.org/W2170939346"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"BACKGROUND:":[0],"Multiple":[1],"sequence":[2,173],"alignments":[3,96,106],"are":[4,37,182,326],"used":[5,240,277],"to":[6,75,123,170,175,201,241,278],"study":[7],"gene":[8,19],"or":[9,31,108,174],"protein":[10],"function,":[11],"phylogenetic":[12],"relations,":[13],"genome":[14],"evolution":[15],"hypotheses":[16],"and":[17,49,54,92,156,207,229,312],"even":[18],"polymorphisms.":[20],"Virtually":[21],"without":[22],"exception,":[23],"all":[24],"available":[25,331],"tools":[26],"focus":[27],"on":[28,102,128,212],"conserved":[29,91,98],"segments":[30],"residues.":[32],"Small":[33],"divergent":[34,93,281,320],"regions,":[35,140],"however,":[36],"biologically":[38],"important":[39],"for":[40,88,137,253,267],"specific":[41,52,243],"quantitative":[42],"polymerase":[43,244],"chain":[44,245],"reaction,":[45],"genotyping,":[46],"molecular":[47],"markers":[48],"preparation":[50],"of":[51,90,97,114,117,150,291,317],"antibodies,":[53],"yet":[55],"have":[56,124,233,295],"received":[57],"little":[58],"attention.":[59],"As":[60],"a":[61,85,115,125,185,213,221,260],"consequence,":[62],"they":[63],"must":[64],"be":[65,165,218,238,276],"selected":[66],"empirically":[67],"by":[68,259,298],"the":[69,129,143,147,153,159,171,271,318],"researcher.":[70],"AlignMiner":[71,83,132,236,274,328],"has":[72],"been":[73,296],"developed":[74,188],"fill":[76],"this":[77],"gap":[78],"in":[79,95,184,189,224],"bioinformatic":[80],"analyses.":[81],"RESULTS:":[82],"is":[84,205,257,303,329],"Web-based":[86],"application":[87],"detection":[89],"regions":[94,151,163,282],"sequences,":[99],"focusing":[100],"particularly":[101],"divergence.":[103],"It":[104],"accepts":[105],"(protein":[107],"nucleic":[109],"acid)":[110],"obtained":[111],"using":[112],"any":[113],"variety":[116],"algorithms,":[118],"which":[119,191],"does":[120],"not":[121,199],"appear":[122],"significant":[126],"impact":[127],"final":[130],"results.":[131],"uses":[133],"different":[134,214,289],"scoring":[135,285],"methods":[136,286],"assessing":[138],"conserved/divergent":[139],"Entropy":[141],"being":[142,158],"method":[144],"that":[145,235,262,287,305],"provides":[146,192],"highest":[148],"number":[149],"with":[152,168],"greatest":[154],"length,":[155],"Weighted":[157],"most":[160],"restrictive.":[161],"Conserved/divergent":[162],"can":[164,217,237,275],"generated":[166],"either":[167],"respect":[169],"consensus":[172],"one":[176],"master":[177],"sequence.":[178],"The":[179],"resulting":[180],"data":[181],"presented":[183],"graphical":[186],"interface":[187],"AJAX,":[190],"remarkable":[193],"user":[194,222],"interaction":[195],"capabilities.":[196],"Users":[197],"do":[198],"need":[200],"wait":[202],"until":[203],"execution":[204],"complete":[206],"can.even":[208],"inspect":[209],"their":[210],"results":[211],"computer.":[215],"Data":[216],"downloaded":[219],"onto":[220],"disk,":[223],"standard":[225],"formats.":[226],"In":[227],"silico":[228],"experimental":[230,299],"proof-of-concept":[231],"cases":[232],"shown":[234],"successfully":[239],"designing":[242,268],"reaction":[246],"primers":[247,269],"as":[248,250],"well":[249],"potential":[251],"epitopes":[252],"antibodies.":[254],"Primer":[255],"design":[256],"assisted":[258],"module":[261],"deploys":[263],"several":[264,284],"oligonucleotide":[265],"parameters":[266],"\"on":[270],"fly\".":[272],"CONCLUSIONS:":[273],"reliably":[279],"detect":[280],"via":[283],"provide":[288],"levels":[290],"selectivity.":[292],"Its":[293],"predictions":[294],"verified":[297],"means.":[300],"Hence,":[301],"it":[302],"expected":[304],"its":[306],"usage":[307],"will":[308],"save":[309],"researchers'":[310],"time":[311],"ensure":[313],"an":[314],"objective":[315],"selection":[316],"best-possible":[319],"region":[321],"when":[322],"closely":[323],"related":[324],"sequences":[325],"analysed.":[327],"freely":[330],"at":[332],"http://www.scbi.uma.es/alignminer.":[333]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}