{"id":"https://openalex.org/W2160206342","doi":"https://doi.org/10.1093/bioinformatics/btg007","title":"Wrapping up BLAST and other applications for use on Unix clusters","display_name":"Wrapping up BLAST and other applications for use on Unix clusters","publication_year":2003,"publication_date":"2003-02-12","ids":{"openalex":"https://openalex.org/W2160206342","doi":"https://doi.org/10.1093/bioinformatics/btg007","mag":"2160206342","pmid":"https://pubmed.ncbi.nlm.nih.gov/12584141"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/441/48903832/bioinformatics_19_3_441.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/441/48903832/bioinformatics_19_3_441.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003377656","display_name":"Karsten Hokamp","orcid":"https://orcid.org/0000-0001-7464-2370"},"institutions":[{"id":"https://openalex.org/I205274468","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19","country_code":"IE","type":"education","lineage":["https://openalex.org/I205274468"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Karsten Hokamp","raw_affiliation_strings":["Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. karsten@oscar.gen.tcd.ie","Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. karsten@oscar.gen.tcd.ie","institution_ids":["https://openalex.org/I205274468"]},{"raw_affiliation_string":"Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland and","institution_ids":["https://openalex.org/I205274468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004065601","display_name":"Denis C. Shields","orcid":"https://orcid.org/0000-0003-4015-2474"},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Denis C. Shields","raw_affiliation_strings":["Department of Clinical Pharmacology, Royal College of Surgeons in Ireland, 123 Stephen's Green, Dublin 2, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Pharmacology, Royal College of Surgeons in Ireland, 123 Stephen's Green, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058698418","display_name":"Kenneth H. Wolfe","orcid":"https://orcid.org/0000-0003-4992-4979"},"institutions":[{"id":"https://openalex.org/I205274468","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19","country_code":"IE","type":"education","lineage":["https://openalex.org/I205274468"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Kenneth H. Wolfe","raw_affiliation_strings":["Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland and","institution_ids":["https://openalex.org/I205274468"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013735262","display_name":"Daniel R. Caffrey","orcid":null},"institutions":[{"id":"https://openalex.org/I142762351","display_name":"Royal College of Surgeons in Ireland","ror":"https://ror.org/01hxy9878","country_code":"IE","type":"education","lineage":["https://openalex.org/I142762351"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Daniel R. Caffrey","raw_affiliation_strings":["Department of Clinical Pharmacology, Royal College of Surgeons in Ireland, 123 Stephen's Green, Dublin 2, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Pharmacology, Royal College of Surgeons in Ireland, 123 Stephen's Green, Dublin 2, Ireland","institution_ids":["https://openalex.org/I142762351"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.1857,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.9488202,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":"3","first_page":"441","last_page":"442"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10742","display_name":"Peer-to-Peer Network Technologies","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10742","display_name":"Peer-to-Peer Network Technologies","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9900000095367432,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10679","display_name":"Service-Oriented Architecture and Web Services","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/unix","display_name":"Unix","score":0.9475851058959961},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6901943683624268},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4385776221752167},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41230320930480957},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.38952434062957764},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3414066433906555}],"concepts":[{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.9475851058959961},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6901943683624268},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4385776221752167},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41230320930480957},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.38952434062957764},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3414066433906555}],"mesh":[{"descriptor_ui":"D003195","descriptor_name":"Computer Communication Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003195","descriptor_name":"Computer Communication Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003195","descriptor_name":"Computer Communication Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btg007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/441/48903832/bioinformatics_19_3_441.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:12584141","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12584141","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:10.1.1.103.3544","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.3544","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://wolfe.gen.tcd.ie/wrapper/downloads/mollusc_wrapid/mollusc_wrapid_corrected.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/441/48903832/bioinformatics_19_3_441.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"},{"id":"https://openalex.org/F4320320864","display_name":"Trinity College Dublin","ror":"https://ror.org/02tyrky19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160206342.pdf","grobid_xml":"https://content.openalex.org/works/W2160206342.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W53898165","https://openalex.org/W1605746882","https://openalex.org/W1969451865","https://openalex.org/W2157975034","https://openalex.org/W2158714788","https://openalex.org/W2162993740"],"related_works":["https://openalex.org/W3053791662","https://openalex.org/W2370505686","https://openalex.org/W3158820933","https://openalex.org/W2144237141","https://openalex.org/W2486626696","https://openalex.org/W3123018244","https://openalex.org/W2788290641","https://openalex.org/W2539062483","https://openalex.org/W3170324660","https://openalex.org/W2354663878"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"We":[2],"have":[3],"developed":[4,52],"two":[5],"programs":[6,41],"that":[7],"speed":[8],"up":[9],"common":[10],"bioinformatic":[11],"applications":[12],"by":[13],"spreading":[14],"them":[15],"across":[16],"a":[17,21,30,56,65],"UNIX":[18],"cluster.(1)":[19],"BLAST.pm,":[20],"new":[22],"module":[23],"for":[24,33],"the":[25],"\u2018MOLLUSC\u2019":[26],"package.":[27],"(2)":[28],"WRAPID,":[29],"simple":[31],"tool":[32],"parallelizing":[34],"large":[35],"numbers":[36],"of":[37,40],"small":[38],"instances":[39],"such":[42],"as":[43],"BLAST,":[44],"FASTA":[45],"and":[46,60,68],"CLUSTALW.":[47],"Availability:":[48],"The":[49],"packages":[50],"were":[51],"in":[53],"Perl":[54],"on":[55],"20-node":[57],"Linux":[58],"cluster":[59],"are":[61],"provided":[62],"together":[63],"with":[64],"configuration":[66],"script":[67],"documentation.":[69],"They":[70],"can":[71],"be":[72],"freely":[73],"downloaded":[74],"from":[75],"http://wolfe.gen.tcd.ie/wrapper":[76],"Contact:":[77],"daniel_r_caffrey@cambridge.pfizer.comkarsten@oscar.gen.tcd.ie":[78],"*":[79],"These":[80],"authors":[81],"contributed":[82],"equally":[83],"to":[84],"this":[85],"work.":[86],"\u2020":[87],"Current":[88],"Address:":[89],"Pfizer":[90],"Discovery":[91],"Technology":[92],"Center,":[93],"620":[94],"Memorial":[95],"Drive,":[96],"Cambridge,":[97],"MA":[98],"02139,":[99],"USA.":[100]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
