{"id":"https://openalex.org/W2008756389","doi":"https://doi.org/10.1093/bib/bbn037","title":"Problems and Solutions in Biological Sequence Analysis * Mark Borodovsky, Svetlana Ekisheva","display_name":"Problems and Solutions in Biological Sequence Analysis * Mark Borodovsky, Svetlana Ekisheva","publication_year":2008,"publication_date":"2008-07-11","ids":{"openalex":"https://openalex.org/W2008756389","doi":"https://doi.org/10.1093/bib/bbn037","mag":"2008756389"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbn037","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbn037","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009657521","display_name":"Mihaela Pertea","orcid":"https://orcid.org/0000-0003-0762-8637"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. Pertea","raw_affiliation_strings":["Assistant Research Faculty, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA","Assistant Research Faculty, Center for Bioinformatics and Computational Biology,University of Maryland, College Park, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Assistant Research Faculty, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"Assistant Research Faculty, Center for Bioinformatics and Computational Biology,University of Maryland, College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009657521"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07844569,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"9","issue":"6","first_page":"550","last_page":"551"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9890000224113464,"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":0.9890000224113464,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9625999927520752,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9284999966621399,"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/sequence","display_name":"Sequence (biology)","score":0.6889222860336304},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4887818992137909},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16533565521240234},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08071479201316833}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6889222860336304},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4887818992137909},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16533565521240234},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08071479201316833}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bib/bbn037","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbn037","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"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/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Since":[0],"its":[1,428],"first":[2,130,359],"publication":[3],"in":[4,116,151,164,252,300,310,317,339,360,371,443,475,501,557,595],"1998,":[5],"Biological":[6],"Sequence":[7],"Analysis":[8],"(BSA)":[9],"by":[10,27,356],"Durbin":[11],"et":[12],"al.":[13],"has":[14],"become":[15],"a":[16,37,93,121,259,314,364,420,450,580,596],"standard":[17],"textbook":[18],"for":[19,82,210,274,326,440,453,498,524],"teaching":[20],"bioinformatics.":[21],"Part":[22],"of":[23,34,39,53,96,124,137,159,195,213,223,248,282,287,304,348,363,374,382,395,401,404,419,427,446,470,517,543,562,583,600,603],"the":[24,31,44,50,83,113,129,140,157,203,211,231,239,275,283,291,297,324,336,346,349,361,372,393,399,402,405,417,425,431,444,468,487,494,508,515,544,559,563,601],"resources":[25],"offered":[26],"BSA":[28,117,165,253,545],"to":[29,43,47,103,112,120,139,206,335,466,485,493,592],"understanding":[30,599],"underlying":[32],"principles":[33],"bioinformatics":[35,85,126,584,602],"is":[36,77,256,307,313,333,354,385,457,539,549],"set":[38,123],"workable":[40],"exercises":[41,388,492],"left":[42],"interested":[45,594],"reader":[46],"solve.":[48],"Given":[49],"multidisciplinary":[51],"background":[52],"bioinformatics,":[54,152],"solving":[55],"these":[56],"problems":[57,114,162,173,217,414,585],"requires":[58],"integrating":[59],"knowledge":[60],"from":[61,92,238,434],"various":[62],"fields":[63],"including":[64,243,479],"genetics":[65],"and":[66,73,169,178,186,198,245,271,321,368,389,398,413,424,510,526,577,605],"molecular":[67,519],"biology":[68],"as":[69,71,528,530],"well":[70,529],"mathematics":[72,548],"computer":[74,234],"science.":[75],"This":[76,312,537],"not":[78,108,464,550],"an":[79,342,375,540],"easy":[80],"challenge":[81],"numerous":[84],"students":[86,564],"who":[87],"come":[88],"with":[89,134,258,263,387,416,586],"different":[90,534],"abilities":[91],"wide":[94],"variety":[95],"educational":[97],"backgrounds.":[98],"Therefore":[99],"I":[100,278,322,482,511,589],"was":[101,483],"glad":[102,484],"see":[104,486],"this":[105,153,288,499,572],"book":[106,154,289,509,538,573],"offering":[107],"only":[109,465,495],"step-by-step":[110],"solutions":[111,191],"presented":[115,163,299],"but":[118,221,473,552],"also":[119,474],"large":[122],"additional":[125,172],"problems.":[127],"From":[128],"introductory":[131],"chapter":[132,144,255,433],"dealing":[133,415],"basic":[135],"notions":[136],"probabilities":[138],"more":[141,146,264,491,597],"technical":[142],"final":[143],"on":[145,174,345,370],"complex":[147],"probabilistic":[148,422],"concepts":[149],"used":[150],"follows":[155],"exactly":[156],"structure":[158],"BSA.":[160,301,311,435,502,566],"All":[161],"are":[166,171,225,290,438,462,505],"meticulously":[167],"solved,":[168],"so":[170],"topics":[175,276,391],"concerning":[176],"pairwise":[177,319,383],"multiple":[179],"sequence":[180,460,535,607],"alignments,":[181,320],"hidden":[182],"Markov":[183,366],"models":[184,521],"(HMMs)":[185],"building":[187],"phylogenetic":[188,480],"trees.":[189],"The":[190,302,379],"often":[192],"contain":[193],"generalizations":[194],"particular":[196,421],"cases":[197,478],"interesting":[199],"remarks":[200],"that":[201,280,295,522],"draw":[202],"reader's":[204],"attention":[205,332],"specific":[207],"results":[208],"important":[209,463],"analysis":[212],"biological":[214],"sequences.":[215,411],"Most":[216],"have":[218],"analytical":[219],"solutions,":[220],"some":[222,281],"them":[224],"algorithmic":[226],"examples.":[227],"In":[228],"such":[229],"cases,":[230],"less":[232],"inexperienced":[233],"programmer":[235],"can":[236],"benefit":[237],"Web":[240],"Supplemental":[241],"Materials":[242],"Perl":[244],"C++":[246],"implementations":[247],"those":[249],"algorithms.":[250],"As":[251],"each":[254],"concluded":[257],"\u2018Further":[260],"reading\u2019":[261],"section":[262],"up-to-date":[265],"bibliographical":[266],"references":[267],"illustrating":[268],"theoretical":[269,293,570],"advances":[270],"research":[272],"directions":[273],"presented.":[277,458],"think":[279],"most":[284],"valuable":[285],"parts":[286],"frequent":[292],"introductions":[294],"broaden":[296],"fundamentals":[298,571],"derivation":[303,347],"substitution":[305,352],"matrices":[306],"briefly":[308],"discussed":[309],"critical":[315],"step":[316],"scoring":[318],"commend":[323],"authors":[325,488],"treating":[327],"it":[328,553,591],"thoroughly":[329],"here.":[330],"More":[331,436],"given":[334,439,497],"PAM":[337],"family":[338],"which":[340],"case":[341,445],"ample":[343],"discussion":[344],"amino":[350],"acid":[351],"scores":[353],"followed":[355],"illustrative":[357],"examples":[358],"context":[362,373],"stationary":[365],"model,":[367],"later":[369],"evolutionary":[376],"model":[377,423],"too.":[378],"statistical":[380],"significance":[381],"alignments":[384,461],"addressed":[386],"theory":[390],"describing":[392],"statistics":[394],"high-scoring":[396],"pairs":[397],"distribution":[400],"length":[403],"longest":[406],"common":[407],"word":[408],"between":[409],"random":[410],"Theory":[412],"selection":[418],"estimation":[426,442],"parameters":[429,469],"expand":[430],"HMM":[432],"details":[437],"parameter":[441],"profile":[447,471],"HMMs":[448],"where":[449],"discrimination":[451],"method":[452],"weighting":[454],"training":[455],"sequences":[456],"Multiple":[459],"estimate":[467],"HMMs,":[472],"many":[476],"other":[477],"inferences.":[481],"add":[489],"three":[490],"one":[496],"topic":[500],"Probabilistic":[503],"interpretations":[504],"abundant":[506],"throughout":[507],"found":[512],"especially":[513],"useful":[514],"treatment":[516],"realistic":[518],"evolution":[520],"allow":[523],"insertions":[525],"deletions":[527],"variable":[531],"rates":[532],"at":[533],"sites.":[536],"excellent":[541],"companion":[542],"book.":[546],"Its":[547],"simple":[551,581],"would":[554],"certainly":[555],"help":[556],"developing":[558],"mathematical":[560],"ability":[561],"studying":[565],"By":[567],"introducing":[568],"detailed":[569],"extends":[574],"BSA's":[575],"domain":[576],"goes":[578],"beyond":[579],"collection":[582],"accompanying":[587],"solutions.":[588],"recommend":[590],"anyone":[593],"in-depth":[598],"DNA":[604],"protein":[606],"analysis.":[608]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
