{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T17:46:57Z","timestamp":1775152017005,"version":"3.50.1"},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,4,8]],"date-time":"2005-04-08T00:00:00Z","timestamp":1112918400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,4,8]],"date-time":"2005-04-08T00:00:00Z","timestamp":1112918400000},"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>BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/liru.ars.usda.gov\/mainbioinformatics.html\">http:\/\/liru.ars.usda.gov\/mainbioinformatics.html<\/jats:ext-link>. With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-93","type":"journal-article","created":{"date-parts":[[2005,4,9]],"date-time":"2005-04-09T06:15:47Z","timestamp":1113027347000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":104,"title":["Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)"],"prefix":"10.1186","volume":"6","author":[{"given":"Scot E","family":"Dowd","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joaquin","family":"Zaragoza","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier R","family":"Rodriguez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melvin J","family":"Oliver","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paxton R","family":"Payton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,4,8]]},"reference":[{"key":"418_CR1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"S Altschul","year":"1990","unstructured":"Altschul S, Gish W, Miller W, Myers E, Lipman DJ: Basic Local Alignment Search Tool. Journal of Molecular Biology 1990, 215: 403\u2013410. 10.1006\/jmbi.1990.9999","journal-title":"Journal of Molecular Biology"},{"key":"418_CR2","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 J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389\u2013402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"418_CR3","volume-title":"WU-BLAST","author":"W Gish","year":"1996","unstructured":"Gish W: WU-BLAST.1996. [http:\/\/blast.wustl.edu]"},{"key":"418_CR4","volume-title":"ClusterWorld 2003 conference","author":"A Darling","year":"2003","unstructured":"Darling A, Carey L, Feng W: The Design, Implementation, and Evaluation of mpiBLAST. ClusterWorld 2003 conference 2003. [http:\/\/mpiblast.lanl.gov\/]"},{"key":"418_CR5","unstructured":"BLAST++[http:\/\/xena1.ddns.comp.nus.edu.sg\/~genesis\/blast++\/]"},{"key":"418_CR6","unstructured":"DeCypherBLAST\u2122[http:\/\/www.timelogic.com\/decypher_blast.html]"},{"key":"418_CR7","volume-title":"Publication pending","author":"SE Dowd","year":"2004","unstructured":"Dowd SE, Rodriguez JR, Khurana V, Sobolewski M, Soorinarayanan S: S-BLAST: Federated BLAST Using Sorcer. Publication pending 2004. [http:\/\/liru.ars.usda.gov]"},{"issue":"5","key":"418_CR8","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1093\/bioinformatics\/18.5.765","volume":"18","author":"JD Grant","year":"2002","unstructured":"Grant JD, Dunbrack RL, Manion FJ, Ochs MF: BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinformatics 2002, 18(5):765\u20136. 10.1093\/bioinformatics\/18.5.765","journal-title":"Bioinformatics"},{"key":"418_CR9","unstructured":"StarBLAST[http:\/\/www.dnastar.com]"},{"key":"418_CR10","unstructured":"Condor BLAST[http:\/\/www.cs.wisc.edu\/condor\/tools\/BLAST\/]"},{"key":"418_CR11","unstructured":"Soap-HT-BLAST[http:\/\/mammoth.bii.a-star.edu.sg\/webservices\/htblast\/index.html]"},{"key":"418_CR12","unstructured":"Paracel[http:\/\/www.paracel.com]"},{"key":"418_CR13","unstructured":"W.ND-BLAST[http:\/\/liru.ars.usda.gov]"},{"key":"418_CR14","unstructured":"NCBI BLAST[http:\/\/www.ncbi.nlm.nih.gov\/BLAST\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-93.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-93\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-93.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:10:33Z","timestamp":1728303033000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-93"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4,8]]},"references-count":14,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["418"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-93","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,4,8]]},"assertion":[{"value":"1 November 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 April 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 April 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"93"}}