{"id":"https://openalex.org/W1563772569","doi":"https://doi.org/10.1186/1471-2105-7-185","title":"Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server","display_name":"Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server","publication_year":2006,"publication_date":"2006-04-03","ids":{"openalex":"https://openalex.org/W1563772569","doi":"https://doi.org/10.1186/1471-2105-7-185","mag":"1563772569","pmid":"https://pubmed.ncbi.nlm.nih.gov/16584563"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-185","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-185","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-185","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-185","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054449714","display_name":"H. Alexander Ebhardt","orcid":"https://orcid.org/0000-0001-9019-8388"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"H Alexander Ebhardt","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, B.C., Canada. aebhardt@sfu.ca","Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, B.C., Canada. aebhardt@sfu.ca","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049270004","display_name":"Kay C. Wiese","orcid":"https://orcid.org/0000-0003-4507-1892"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Kay C Wiese","raw_affiliation_strings":["School of Computing Science, Simon Fraser University Surrey, 13450 102nd Ave, V3T 5X3, Surrey, B.C., Canada","School of Computing Science, Simon Fraser University Surrey, Surrey, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University Surrey, 13450 102nd Ave, V3T 5X3, Surrey, B.C., Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"School of Computing Science, Simon Fraser University Surrey, Surrey, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002938273","display_name":"Peter J. Unrau","orcid":"https://orcid.org/0000-0003-1392-6948"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Peter J Unrau","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, B.C., Canada","Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, B.C., Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054449714"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.248,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.82857357,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"1","first_page":"185","last_page":"185"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.2071000039577484,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.2071000039577484,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.12460000067949295,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.06129999831318855,"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/cloning","display_name":"Cloning (programming)","score":0.7409060001373291},{"id":"https://openalex.org/keywords/substring","display_name":"Substring","score":0.702215850353241},{"id":"https://openalex.org/keywords/insert","display_name":"Insert (composites)","score":0.5801399946212769},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5277303457260132},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4992969036102295},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.49042627215385437},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4793975353240967},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.456983357667923},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4549001455307007},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.4241219758987427},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38036689162254333},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32998141646385193},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.21509671211242676},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20339909195899963},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.1793491244316101},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16413912177085876}],"concepts":[{"id":"https://openalex.org/C121050878","wikidata":"https://www.wikidata.org/wiki/Q5135020","display_name":"Cloning (programming)","level":2,"score":0.7409060001373291},{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.702215850353241},{"id":"https://openalex.org/C2780098074","wikidata":"https://www.wikidata.org/wiki/Q6037362","display_name":"Insert (composites)","level":2,"score":0.5801399946212769},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5277303457260132},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4992969036102295},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.49042627215385437},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4793975353240967},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.456983357667923},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4549001455307007},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.4241219758987427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38036689162254333},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32998141646385193},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.21509671211242676},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20339909195899963},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.1793491244316101},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16413912177085876},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","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":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003001","descriptor_name":"Cloning, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003001","descriptor_name":"Cloning, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003001","descriptor_name":"Cloning, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-7-185","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-185","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-185","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16584563","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16584563","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:8c0204b2bfb94f0ba2f4107fd70030a1","is_oa":true,"landing_page_url":"https://doaj.org/article/8c0204b2bfb94f0ba2f4107fd70030a1","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 185 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:209573","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1450305","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1450305","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1450305","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:summit.sfu.ca:11000","is_oa":true,"landing_page_url":"http://summit.sfu.ca/item/11000","pdf_url":null,"source":{"id":"https://openalex.org/S4306400490","display_name":"Summit (Simon Fraser University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I18014758","host_organization_name":"Simon Fraser University","host_organization_lineage":["https://openalex.org/I18014758"],"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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-185","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-185","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-185","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.800000011920929}],"awards":[],"funders":[{"id":"https://openalex.org/F4320319965","display_name":"Michael Smith Health Research BC","ror":"https://ror.org/020x39229"},{"id":"https://openalex.org/F4320322551","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1563772569.pdf","grobid_xml":"https://content.openalex.org/works/W1563772569.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W393022889","https://openalex.org/W1507799491","https://openalex.org/W1584433563","https://openalex.org/W1978337436","https://openalex.org/W1993799748","https://openalex.org/W1994814273","https://openalex.org/W1999338744","https://openalex.org/W2001911979","https://openalex.org/W2020878700","https://openalex.org/W2021735982","https://openalex.org/W2030120875","https://openalex.org/W2032323486","https://openalex.org/W2040191060","https://openalex.org/W2041953113","https://openalex.org/W2050801344","https://openalex.org/W2062469063","https://openalex.org/W2088930981","https://openalex.org/W2090438401","https://openalex.org/W2113349324","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2123970063","https://openalex.org/W2131841865","https://openalex.org/W2136145671","https://openalex.org/W2150770935","https://openalex.org/W2154171946","https://openalex.org/W2157551654","https://openalex.org/W2158714788","https://openalex.org/W2167557255","https://openalex.org/W2415046415","https://openalex.org/W2488335160","https://openalex.org/W4249371825"],"related_works":["https://openalex.org/W1583922594","https://openalex.org/W2998448420","https://openalex.org/W3095957182","https://openalex.org/W2385470386","https://openalex.org/W2550930617","https://openalex.org/W2379603891","https://openalex.org/W2129713745","https://openalex.org/W2581600691","https://openalex.org/W2183615490","https://openalex.org/W2028473472"],"abstract_inverted_index":{"BACKGROUND:":[0],"DNA":[1,143,207,333,365,386],"sequencing":[2,46,144,208,366],"is":[3,22,127,148,161,256,353],"used":[4,74,201,284],"ubiquitously:":[5],"from":[6,70,211,236],"deciphering":[7],"genomes":[8],"to":[9,28,49,75,110,119,176,187,194,203,229,318,361,380],"determining":[10],"the":[11,24,30,45,71,79,181,185,189,244,341,351],"primary":[12],"sequence":[13,32,65,197,289,298],"of":[14,20,33,37,47,51,184,206,221,234,247,253,288,299,304,315,383],"small":[15],"RNAs":[16],"(smRNAs).":[17],"The":[18,154,301],"cloning":[19,42,90,131,214,274,374,387],"smRNAs":[21,235],"currently":[23,262],"most":[25],"conventional":[26],"method":[27],"determine":[29],"actual":[31],"these":[34],"important":[35],"regulators":[36],"gene":[38],"expression.":[39],"Typical":[40],"smRNA":[41,52,80,89,102,114,130,158,191,213,273,373],"projects":[43,275],"involve":[44],"hundreds":[48],"thousands":[50],"clones":[53],"that":[54],"are":[55,171],"delimited":[56],"at":[57],"their":[58,307],"5'":[59],"and":[60,77,112,166,193,249,261,306,320,344,348,385],"3'":[61],"ends":[62],"by":[63,150],"fixed":[64],"regions.":[66],"These":[67,169],"primers":[68],"result":[69],"biochemical":[72],"protocol":[73],"isolate":[76],"convert":[78],"into":[81],"clonable":[82],"PCR":[83],"products.":[84],"Recently":[85],"we":[86,116,226],"completed":[87],"a":[88,128,142,164,297,310,325,381],"project":[91],"involving":[92],"tobacco":[93],"plants,":[94],"where":[95,291],"analysis":[96,220,290],"was":[97,268,369],"required":[98],"for":[99,138,270,285,372],"approximately":[100,237],"700":[101,238],"sequences.":[103],"Finding":[104],"no":[105],"easily":[106],"accessible":[107],"research":[108],"tool":[109,328],"enter":[111],"analyze":[113,204],"sequences":[115],"developed":[117],"Ebbie":[118,126,202,255,267,281,335,368],"assist":[120],"us":[121],"with":[122,276],"our":[123],"study.":[124],"RESULTS:":[125],"semi-automated":[129],"data":[132,209],"processing":[133],"algorithm,":[134],"which":[135,147],"initially":[136],"searches":[137],"any":[139,286,330],"substring":[140],"within":[141],"text":[145],"file,":[146],"flanked":[149],"two":[151,292],"constant":[152,293],"strings.":[153],"substring,":[155],"also":[156,336],"termed":[157],"or":[159],"insert,":[160],"stored":[162],"in":[163,309,329],"MySQL":[165,311],"BlastN":[167,175,313],"database.":[168],"inserts":[170,223,317],"then":[172],"compared":[173],"using":[174,224,332],"locally":[177],"installed":[178,354],"databases":[179,322],"allowing":[180],"rapid":[182],"comparison":[183,314],"insert":[186],"both":[188],"growing":[190],"database":[192,239,279],"other":[195],"static":[196,321],"databases.":[198],"Our":[199],"laboratory":[200,331],"scores":[205],"originating":[210],"an":[212],"project.":[215],"Through":[216],"its":[217,356],"built-in":[218],"instant":[219],"all":[222],"BlastN,":[225],"were":[227],"able":[228],"quickly":[230],"identify":[231],"33":[232],"groups":[233],"entries.":[240,280],"This":[241],"clustering":[242],"allowed":[243],"easy":[245],"identification":[246],"novel":[248],"highly":[250],"expressed":[251],"clusters":[252],"smRNAs.":[254],"available":[257],"under":[258],"GNU":[259],"GPL":[260],"implemented":[263],"on":[264],"http://bioinformatics.org/ebbie/.":[265],"CONCLUSION:":[266],"designed":[269,371],"medium":[271],"sized":[272],"about":[277],"1,000":[278],"can":[282,358,377],"be":[283,359,378],"type":[287],"primer":[294],"regions":[295],"flank":[296],"interest.":[300],"reliable":[302],"storage":[303],"inserts,":[305],"annotation":[308,347],"database,":[312],"new":[316,327,364],"dynamic":[319],"make":[323],"it":[324],"powerful":[326],"sequencing.":[334],"prevents":[337],"manual":[338],"mistakes":[339],"during":[340],"excision":[342],"process":[343],"speeds":[345],"up":[346],"data-entry.":[349],"Once":[350],"server":[352],"locally,":[355],"access":[357],"restricted":[360],"protect":[362],"sensitive":[363],"data.":[367],"primarily":[370],"projects,":[375],"but":[376],"applied":[379],"variety":[382],"RNA":[384],"projects.":[388]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}