{"id":"https://openalex.org/W2065989019","doi":"https://doi.org/10.1145/2147805.2147815","title":"Detecting fuzzy amino acid tandem repeats in protein sequences","display_name":"Detecting fuzzy amino acid tandem repeats in protein sequences","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2065989019","doi":"https://doi.org/10.1145/2147805.2147815","mag":"2065989019"},"language":"en","primary_location":{"id":"doi:10.1145/2147805.2147815","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147815","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5028551838","display_name":"Marco Pellegrini","orcid":"https://orcid.org/0000-0003-3151-9481"},"institutions":[{"id":"https://openalex.org/I4210130157","display_name":"Institute of Informatics and Telematics","ror":"https://ror.org/02gdcn153","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210130157","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Pellegrini","raw_affiliation_strings":["Istituto di Informatica e Telematica, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Istituto di Informatica e Telematica, Pisa, Italy","institution_ids":["https://openalex.org/I4210130157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005528176","display_name":"M. Elena Renda","orcid":"https://orcid.org/0000-0001-5485-0084"},"institutions":[{"id":"https://openalex.org/I4210130157","display_name":"Institute of Informatics and Telematics","ror":"https://ror.org/02gdcn153","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210130157","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"M. Elena Renda","raw_affiliation_strings":["Istituto di Informatica e Telematica, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Istituto di Informatica e Telematica, Pisa, Italy","institution_ids":["https://openalex.org/I4210130157"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080972873","display_name":"Alessio Vecchio","orcid":"https://orcid.org/0000-0001-6894-7338"},"institutions":[{"id":"https://openalex.org/I4210126460","display_name":"Fondazione Stella Maris","ror":"https://ror.org/02w8ez808","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210126460","https://openalex.org/I4210153126"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessio Vecchio","raw_affiliation_strings":["Universit\u00e0 degli Studi di Pisa, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e0 degli Studi di Pisa, Pisa, Italy","institution_ids":["https://openalex.org/I4210126460"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16444624,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"87","last_page":"95"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9972000122070312,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9972000122070312,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9857000112533569,"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/tandem-repeat","display_name":"Tandem repeat","score":0.7380480170249939},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.734248697757721},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5978933572769165},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5711486339569092},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5417232513427734},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5283632874488831},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.4554027318954468},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.441040962934494},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.437549352645874},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.42984652519226074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40766268968582153},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38852718472480774},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38711005449295044},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3309077322483063},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0751112699508667},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06641256809234619}],"concepts":[{"id":"https://openalex.org/C27149982","wikidata":"https://www.wikidata.org/wiki/Q3456514","display_name":"Tandem repeat","level":4,"score":0.7380480170249939},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.734248697757721},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5978933572769165},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5711486339569092},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5417232513427734},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5283632874488831},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.4554027318954468},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.441040962934494},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.437549352645874},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.42984652519226074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40766268968582153},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38852718472480774},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38711005449295044},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3309077322483063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0751112699508667},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06641256809234619},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2147805.2147815","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147815","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:arpi.unipi.it:11568/148042","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/148042","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8890333172","display_name":null,"funder_award_id":"N 223920","funder_id":"https://openalex.org/F4320334960","funder_display_name":"Seventh Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320334960","display_name":"Seventh Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1593563200","https://openalex.org/W1606551583","https://openalex.org/W1873119440","https://openalex.org/W1938523069","https://openalex.org/W1967195968","https://openalex.org/W1987393189","https://openalex.org/W1991731239","https://openalex.org/W2008560636","https://openalex.org/W2015739888","https://openalex.org/W2016685368","https://openalex.org/W2022366485","https://openalex.org/W2024369500","https://openalex.org/W2046239250","https://openalex.org/W2066688961","https://openalex.org/W2073127551","https://openalex.org/W2094104050","https://openalex.org/W2094519647","https://openalex.org/W2096366535","https://openalex.org/W2105961968","https://openalex.org/W2106532429","https://openalex.org/W2116426890","https://openalex.org/W2126597349","https://openalex.org/W2128591967","https://openalex.org/W2129328366","https://openalex.org/W2131239524","https://openalex.org/W2132505033","https://openalex.org/W2148099726","https://openalex.org/W2157736844","https://openalex.org/W2162085776","https://openalex.org/W2164797647","https://openalex.org/W2285941358","https://openalex.org/W2295428206","https://openalex.org/W4231916799","https://openalex.org/W6628896446","https://openalex.org/W6636374848"],"related_works":["https://openalex.org/W2114077379","https://openalex.org/W2161189461","https://openalex.org/W3107404305","https://openalex.org/W3132261088","https://openalex.org/W2972635466","https://openalex.org/W2803517106","https://openalex.org/W2106830745","https://openalex.org/W1994428965","https://openalex.org/W1967142621","https://openalex.org/W4240507550"],"abstract_inverted_index":{"Tandem":[0],"repetitions":[1,25],"within":[2],"protein":[3,97],"amino":[4,98,112],"acid":[5,99,113],"sequences":[6,114],"often":[7,72],"correspond":[8],"to":[9,35],"regular":[10],"secondary":[11],"structures":[12,56,124],"and":[13,21,39,69],"form":[14],"multi-repeat":[15],"3D":[16],"assemblies":[17],"of":[18,28,54,91],"varied":[19],"size":[20],"function.":[22],"Developing":[23],"internal":[24],"is":[26,46,62,71],"one":[27],"the":[29,102,116],"evolutionary":[30,42],"mechanisms":[31],"that":[32,107],"proteins":[33],"employ":[34],"adapt":[36],"their":[37],"structure":[38,68],"function":[40,70],"under":[41,75],"pressure.":[43],"While":[44],"there":[45],"keen":[47],"interest":[48],"in":[49,96],"understanding":[50],"such":[51],"phenomena,":[52],"detection":[53,90],"repeating":[55],"based":[57],"only":[58],"on":[59],"sequence":[60,77],"analysis":[61],"considered":[63],"an":[64],"arduous":[65],"task,":[66],"since":[67],"preserved":[73],"even":[74],"considerable":[76],"divergence.":[78],"In":[79,101],"this":[80],"paper":[81],"we":[82,105,119],"present":[83],"PTRStalker,":[84],"a":[85],"new":[86],"algorithm":[87],"for":[88],"ab-initio":[89],"very":[92],"fuzzy":[93],"tandem":[94],"repeats":[95],"sequences.":[100],"reported":[103],"results":[104],"show":[106],"by":[108,127],"feeding":[109],"PTRStalker":[110],"with":[111],"from":[115],"UniProtKB/Swiss-Prot":[117],"database":[118],"detect":[120],"novel":[121],"tandemly":[122],"repeated":[123],"not":[125],"captured":[126],"other":[128],"state-of-the-art":[129],"tools.":[130]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
