{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T06:47:43Z","timestamp":1763016463524},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:Different automatic methods of sequence alignments are routinely used as a starting point for homology searches and function inference. Confidence in an alignment probability is one of the major fundamentals of massive automatic genome-scale pairwise comparisons, for clustering of putative orthologs and paralogs, sequenced genome annotation or multiple-genomic tree constructions. Extreme value distribution based on the Karlin\u2013Altschul model, usually advised for large-scale comparisons are not always valid, particularly in the case of comparisons of non-biased with nucleotide-biased genomes (such that of Plasmodium falciparum). Z-values estimates based on Monte Carlo technics, can be calculated experimentally for any alignment output, whatever the method used. Empirically, a Z-value higher than \u223c8 is supposed reasonable to assess that an alignment score is significant, but this arbitrary figure was never theoretically justified.<\/jats:p>\n               <jats:p>Results: In this paper, we used the Bienaym\u00e9\u2013Chebyshev inequality to demonstrate a theorem of the upper limit of an alignment score probability (or P-value). This theorem implies that a computed Z-value is a statistical test, a single-linkage clustering criterion and that 1\/Z-value2 is an upper limit to the probability of an alignment score whatever the actual probability law is. Therefore, this study provides the missing theoretical link between a Z-value cut-off used for an automatic clustering of putative orthologs and\/or paralogs, and the corresponding statistical risk in such genome-scale comparisons (using non-biased or biased genomes).<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg440","type":"journal-article","created":{"date-parts":[[2004,2,27]],"date-time":"2004-02-27T17:23:07Z","timestamp":1077902587000},"page":"534-537","source":"Crossref","is-referenced-by-count":26,"title":["Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of <i>Z<\/i>-value statistics"],"prefix":"10.1093","volume":"20","author":[{"given":"Olivier","family":"Bastien","sequence":"first","affiliation":[]},{"given":"Jean-Christophe","family":"Aude","sequence":"additional","affiliation":[]},{"given":"Sylvaine","family":"Roy","sequence":"additional","affiliation":[]},{"given":"Eric","family":"Mar\u00e9chal","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,1,22]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/4\/534\/48905111\/bioinformatics_20_4_534.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/4\/534\/48905111\/bioinformatics_20_4_534.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:19:56Z","timestamp":1674670796000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/4\/534\/192450"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,1,22]]},"references-count":0,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2004,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg440","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,3,1]]},"published":{"date-parts":[[2004,1,22]]}}}