{"id":"https://openalex.org/W2166119698","doi":"https://doi.org/10.1093/bioinformatics/btn052","title":"The effect of sequence quality on sequence alignment","display_name":"The effect of sequence quality on sequence alignment","publication_year":2008,"publication_date":"2008-02-23","ids":{"openalex":"https://openalex.org/W2166119698","doi":"https://doi.org/10.1093/bioinformatics/btn052","mag":"2166119698","pmid":"https://pubmed.ncbi.nlm.nih.gov/18296747"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn052","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/897/49046341/bioinformatics_24_7_897.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/24/7/897/49046341/bioinformatics_24_7_897.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061545123","display_name":"Ketil Malde","orcid":"https://orcid.org/0000-0001-7381-1849"},"institutions":[{"id":"https://openalex.org/I2802153510","display_name":"Norwegian Institute of Marine Research","ror":"https://ror.org/05vg74d16","country_code":"NO","type":"facility","lineage":["https://openalex.org/I2802153510","https://openalex.org/I4210116418","https://openalex.org/I4210149801"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ketil Malde","raw_affiliation_strings":["Institute of Marine Research, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Marine Research, Bergen, Norway","institution_ids":["https://openalex.org/I2802153510"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5061545123"],"corresponding_institution_ids":["https://openalex.org/I2802153510"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8335,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.73325441,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"24","issue":"7","first_page":"897","last_page":"900"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.879800021648407,"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":0.879800021648407,"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/T11269","display_name":"Algorithms and Data Compression","score":0.008500000461935997,"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"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.00559999980032444,"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/trimming","display_name":"Trimming","score":0.8098368644714355},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6966222524642944},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6658295392990112},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6392303705215454},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6322160959243774},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.6038289666175842},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.597015380859375},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5791858434677124},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5737054347991943},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4975447952747345},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.46364274621009827},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4628339111804962},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3660925030708313},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23566091060638428},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11304685473442078},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10300439596176147},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.08529853820800781}],"concepts":[{"id":"https://openalex.org/C56951928","wikidata":"https://www.wikidata.org/wiki/Q3539213","display_name":"Trimming","level":2,"score":0.8098368644714355},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6966222524642944},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6658295392990112},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6392303705215454},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6322160959243774},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.6038289666175842},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.597015380859375},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5791858434677124},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5737054347991943},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4975447952747345},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.46364274621009827},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4628339111804962},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3660925030708313},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23566091060638428},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11304685473442078},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10300439596176147},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.08529853820800781},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn052","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/897/49046341/bioinformatics_24_7_897.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18296747","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18296747","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:CiteSeerX.psu:10.1.1.560.2835","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.560.2835","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.ii.uib.no/~ketil/bioinformatics/downloads/qualign.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn052","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/7/897/49046341/bioinformatics_24_7_897.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320316989","display_name":"Havforskningsinstituttet","ror":"https://ror.org/05vg74d16"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166119698.pdf","grobid_xml":"https://content.openalex.org/works/W2166119698.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1528782506","https://openalex.org/W1973578915","https://openalex.org/W1985726486","https://openalex.org/W2015292449","https://openalex.org/W2016453697","https://openalex.org/W2055043387","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2101972919","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2153211479","https://openalex.org/W2161113604","https://openalex.org/W2166265186"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2141411672"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,103],"nucleotide":[2],"sequencing":[3],"process":[4],"produces":[5],"not":[6],"only":[7,26,96],"the":[8,41],"sequence":[9],"of":[10,44,78,87],"nucleotides,":[11],"but":[12,22],"also":[13,70,106],"associated":[14],"quality":[15,55],"values.":[16],"Quality":[17],"values":[18,56],"provide":[19],"valuable":[20],"information,":[21],"are":[23],"primarily":[24],"used":[25,73],"for":[27],"trimming":[28],"sequences":[29],"and":[30,61,72,91,118],"generally":[31],"ignored":[32],"in":[33],"subsequent":[34],"analyses.":[35],"RESULTS:":[36],"This":[37],"article":[38],"describes":[39],"how":[40],"scoring":[42],"schemes":[43],"standard":[45,88],"alignment":[46,82,89],"algorithms":[47,115],"can":[48,92,105],"be":[49,93,107],"modified":[50],"to":[51,57,74,109],"take":[52],"into":[53],"account":[54],"produce":[58],"improved":[59],"alignments":[60],"statistically":[62],"more":[63],"accurate":[64],"scores.":[65],"A":[66],"prototype":[67],"implementation":[68],"is":[69,83],"provided,":[71],"post-process":[75],"a":[76,84,97],"set":[77],"BLAST":[79,117],"results.":[80],"Quality-adjusted":[81],"natural":[85],"extension":[86],"methods,":[90],"implemented":[94],"with":[95],"small":[98],"constant":[99],"factor":[100],"performance":[101],"penalty.":[102],"method":[104],"applied":[108],"related":[110],"methods":[111],"including":[112],"heuristic":[113],"search":[114],"like":[116],"FASTA.":[119],"AVAILABILITY:":[120],"http://malde.org/~ketil/qaa.":[121]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}