{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T14:29:23Z","timestamp":1742394563846},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The performance of sequence database search methods is usually judged by receiver operating characteristic (ROC) analysis. The proper interpretation of the results obtained and a fair comparison across different methods critically depends on the properties of the data set used for such an analysis; in particular, each query must have the same number of true positives and true negatives. Here, we present a novel web service based on a dataset specifically designed for ROC analysis and the investigation of alignment quality. The data set is derived from a quantitative classification of protein structures (COPS), while analysis and results are presented through an intuitive web interface. The analysis provides details such as false positives per query, and visualization of the structural similarity between query and targets. Most importantly, results obtained for a specific alignment method are immediately related to those obtained for several popular standard sequence alignment methods.<\/jats:p>\n               <jats:p>Availability: The COPS-Benchmark service is available at http:\/\/benchmark.services.came.sbg.ac.at<\/jats:p>\n               <jats:p>Contact: \u00a0publications@came.sbg.ac.at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp712","type":"journal-article","created":{"date-parts":[[2010,1,16]],"date-time":"2010-01-16T01:14:00Z","timestamp":1263604440000},"page":"574-575","source":"Crossref","is-referenced-by-count":9,"title":["COPS Benchmark: interactive analysis of database search methods"],"prefix":"10.1093","volume":"26","author":[{"given":"Karl","family":"Frank","sequence":"first","affiliation":[{"name":"Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria"}]},{"given":"Markus","family":"Gruber","sequence":"additional","affiliation":[{"name":"Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria"}]},{"given":"Manfred J.","family":"Sippl","sequence":"additional","affiliation":[{"name":"Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria"}]}],"member":"286","published-online":{"date-parts":[[2010,1,15]]},"reference":[{"key":"2023012508030260200_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012508030260200_B2","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1093\/bioinformatics\/16.2.135","article-title":"TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon","volume":"16","author":"Beitz","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012508030260200_B3","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/S0022-2836(02)01371-2","article-title":"COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance","volume":"326","author":"Sadreyev","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2023012508030260200_B4","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1093\/bioinformatics\/btn040","article-title":"On distance and similarity in fold space","volume":"24","author":"Sippl","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508030260200_B5","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/bioinformatics\/btm622","article-title":"A note on difficult structure alignment problems","volume":"24","author":"Sippl","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508030260200_B6","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM-HMM comparison","volume":"21","author":"S\u00f6ding","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508030260200_B7","doi-asserted-by":"crossref","first-page":"W539","DOI":"10.1093\/nar\/gkp411","article-title":"COPS\u2013a novel workbench for explorations in fold space","volume":"37","author":"Suhrer","year":"2009","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/4\/574\/48855811\/bioinformatics_26_4_574.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/4\/574\/48855811\/bioinformatics_26_4_574.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:03:52Z","timestamp":1674633832000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/4\/574\/244810"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,1,15]]},"references-count":7,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2010,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp712","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,2,15]]},"published":{"date-parts":[[2010,1,15]]}}}