{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T20:58:09Z","timestamp":1761512289819},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database.<\/jats:p>\n               <jats:p>Availability: The IndexToolkit is free to use under the open source GNU GPL license. The source code and the compiled binary can be freely accessed through the website . In this website, the more detailed information including screenshots and documentations for users and developers is also available.<\/jats:p>\n               <jats:p>Contact: \u00a0dqli@jdl.ac.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl410","type":"journal-article","created":{"date-parts":[[2006,9,1]],"date-time":"2006-09-01T00:17:55Z","timestamp":1157069875000},"page":"2572-2573","source":"Crossref","is-referenced-by-count":5,"title":["IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics"],"prefix":"10.1093","volume":"22","author":[{"given":"Dequan","family":"Li","sequence":"first","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences 1 \u00a0 1 \u00a0 \u00a0 Beijing 100080, China"},{"name":"Graduate University of Chinese Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen","family":"Gao","sequence":"additional","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences 1 \u00a0 1 \u00a0 \u00a0 Beijing 100080, China"},{"name":"Graduate University of Chinese Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles X.","family":"Ling","sequence":"additional","affiliation":[{"name":"Department of Computer Science, The University of Western Ontario 3 \u00a0 3 \u00a0 \u00a0 Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaobiao","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences 1 \u00a0 1 \u00a0 \u00a0 Beijing 100080, China"},{"name":"Graduate University of Chinese Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruixiang","family":"Sun","sequence":"additional","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences 1 \u00a0 1 \u00a0 \u00a0 Beijing 100080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simin","family":"He","sequence":"additional","affiliation":[{"name":"Institute of Computing Technology, Chinese Academy of Sciences 1 \u00a0 1 \u00a0 \u00a0 Beijing 100080, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,8,31]]},"reference":[{"key":"2023012409235726800_b1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based proteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"key":"2023012409235726800_b2","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"TANDEM: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012409235726800_b3","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1002\/pmic.200300721","article-title":"The International Protein Index: an integrated database for proteomics experiments","volume":"4","author":"Kersey","year":"2004","journal-title":"Proteomics"},{"key":"2023012409235726800_b4","doi-asserted-by":"crossref","first-page":"3049","DOI":"10.1093\/bioinformatics\/bti439","article-title":"pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry","volume":"21","author":"Li","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409235726800_b5","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1093\/bioinformatics\/bti588","article-title":"DBToolkit: processing protein databases for peptide-centric proteomics","volume":"21","author":"Martens","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409235726800_b6","doi-asserted-by":"crossref","first-page":"3931","DOI":"10.1021\/ac0481046","article-title":"Discovering known and unanticipated protein modifications using MS\/MS database searching","volume":"77","author":"Tang","year":"2005","journal-title":"Anal. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/20\/2572\/48841449\/bioinformatics_22_20_2572.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/20\/2572\/48841449\/bioinformatics_22_20_2572.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T10:11:01Z","timestamp":1674555061000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/20\/2572\/218090"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,8,31]]},"references-count":6,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2006,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl410","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,10,15]]},"published":{"date-parts":[[2006,8,31]]}}}