{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T17:36:36Z","timestamp":1774978596063,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":5365,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Basic Research Program of China","doi-asserted-by":"crossref","award":["2006CB910404"],"award-info":[{"award-number":["2006CB910404"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The ratio of nonsynonymous substitution rate (Ka) to synonymous substitution rate (Ks) is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models have been incorporated into several computing methods. We have previously developed a new \u03b3-MYN method by capturing a key dynamic evolution trait of DNA nucleotide sequences, in consideration of varying mutation rates across sites. We now report a further improvement of NG, LWL, MLWL, LPB, MLPB, and YN methods based on an introduction of gamma distribution to illustrate the variation of raw mutation rate over sites. The novelty comes in two ways: (1) we incorporate an optimal gamma distribution shape parameter a into \u03b3-NG, \u03b3-LWL, \u03b3-MLWL, \u03b3-LPB, \u03b3-MLPB, and \u03b3-YN methods; (2) we investigate how variable substitution rates affect the methods that adopt different models as well as the interplay among four evolutional features with respect to Ka\/Ks computations. Our results suggest that variable substitution rates over sites under negative selection exhibit an opposite effect on \u03c9 estimates compared with those under positive selection. We believe that the sensitivity of our new methods has been improved than that of their original methods under diverse conditions and it is advantageous to introduce novel parameters for Ka\/Ks computation.<\/jats:p>","DOI":"10.1016\/s1672-0229(08)60040-6","type":"journal-article","created":{"date-parts":[[2009,11,28]],"date-time":"2009-11-28T02:52:42Z","timestamp":1259376762000},"page":"116-127","source":"Crossref","is-referenced-by-count":57,"title":["How Do Variable Substitution Rates Influence Ka and Ks Calculations?"],"prefix":"10.1093","volume":"7","author":[{"given":"Dapeng","family":"Wang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Song","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"},{"name":"Institute of Computing Technology, Chinese Academy of Sciences , Beijing, 100080 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuhong","family":"He","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Graduate University of Chinese Academy of Sciences , Beijing, 100049 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Songnian","family":"Hu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Yu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing, 100029 , China"},{"name":"Institute of Computing Technology, Chinese Academy of Sciences , Beijing, 100080 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,11,25]]},"reference":[{"key":"2024051008262499300_bib1","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195135848.001.0001","article-title":"Molecular Evolution and Phylogenetics","author":"Nei","year":"2000"},{"key":"2024051008262499300_bib2","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780198567028.001.0001","article-title":"Computational Molecular Evolution","author":"Yang","year":"2006"},{"key":"2024051008262499300_bib3","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S1672-0229(06)60030-2","article-title":"Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates","volume":"4","author":"Zhang","year":"2006","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024051008262499300_bib4","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1093\/oxfordjournals.molbev.a025549","article-title":"Estimating synonymous and nonsynonymous substitution rates","volume":"13","author":"Muse","year":"1996","journal-title":"Mol. 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