{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:14:58Z","timestamp":1728360898963},"reference-count":11,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,6,15]],"date-time":"2005-06-15T00:00:00Z","timestamp":1118793600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,6,15]],"date-time":"2005-06-15T00:00:00Z","timestamp":1118793600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background -<\/jats:title>\n                        <jats:p>Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results -<\/jats:title>\n                        <jats:p>Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion -<\/jats:title>\n                        <jats:p>This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-147","type":"journal-article","created":{"date-parts":[[2005,6,15]],"date-time":"2005-06-15T18:13:37Z","timestamp":1118859217000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system"],"prefix":"10.1186","volume":"6","author":[{"given":"Stephen E","family":"Diener","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas D","family":"Houfek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sam E","family":"Kalat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"DE","family":"Windham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Burke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles","family":"Opperman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralph A","family":"Dean","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,6,15]]},"reference":[{"key":"472_CR1","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1093\/bioinformatics\/18.5.765","volume":"18","author":"JT Grant","year":"2002","unstructured":"Grant JT, Dunbrack RL, Manion FJ, Ochs MF: BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinformatics 2002, 18: 765\u2013766. 10.1093\/bioinformatics\/18.5.765","journal-title":"Bioinformatics"},{"key":"472_CR2","unstructured":"BioPerl Website[http:\/\/www.bioperl.org]"},{"key":"472_CR3","unstructured":"Apache Website[http:\/\/www.apache.org]"},{"key":"472_CR4","unstructured":"PHP Website[http:\/\/www.php.net]"},{"key":"472_CR5","unstructured":"MySQL Website[http:\/\/www.mysql.org]"},{"key":"472_CR6","unstructured":"PBS Website[http:\/\/www.openpbs.org]"},{"issue":"17","key":"472_CR7","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389\u20133402. [http:\/\/www.ncbi.nlm.nih.gov\/blast] 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"472_CR8","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1101\/gr.361602","volume":"12","author":"JE Stajich","year":"2002","unstructured":"Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611\u20138. 10.1101\/gr.361602","journal-title":"Genome Res"},{"issue":"1","key":"472_CR9","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25(1):25\u201329. [http:\/\/www.geneontology.org] 10.1038\/75556","journal-title":"Nat Genet"},{"issue":"5","key":"472_CR10","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1101\/gr.86902","volume":"12","author":"HQ Xie","year":"2002","unstructured":"Xie HQ, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz L: Large-scale protein annotation through gene ontology. Genome Res 2002, 12(5):785\u2013794. 10.1101\/gr.86902","journal-title":"Genome Res"},{"key":"472_CR11","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/S0378-1097(03)00916-9","volume":"230","author":"SE Diener","year":"2004","unstructured":"Diener SE, Dunn-Coleman N, Foreman P, Houfek TD, Teunissen PJM, van Solingen P, Dankmeyer L, Mitchell TK, Ward M, Dean RA: Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei . FEMS Microbiol Lett 2004, 230: 275\u2013282. 10.1016\/S0378-1097(03)00916-9","journal-title":"FEMS Microbiol Lett"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-147.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-147\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-147.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:13:15Z","timestamp":1728303195000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-147"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,6,15]]},"references-count":11,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["472"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-147","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2005,6,15]]},"assertion":[{"value":"10 December 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 June 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 June 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"147"}}