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題名 Alignathon: A competitive assessment of whole genome alignment methods 作者 張家銘 貢獻者 資科系 日期 2014-10 上傳時間 30-May-2016 17:24:03 (UTC+8) 摘要 Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. 關聯 Genome Research, Vol.24, pp.2077-2089 資料類型 article DOI http://dx.doi.org/10.1101/gr.174920.114 dc.contributor 資科系 dc.creator (作者) 張家銘 zh_TW dc.date (日期) 2014-10 dc.date.accessioned 30-May-2016 17:24:03 (UTC+8) - dc.date.available 30-May-2016 17:24:03 (UTC+8) - dc.date.issued (上傳時間) 30-May-2016 17:24:03 (UTC+8) - dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/97012 - dc.description.abstract (摘要) Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. dc.format.extent 1919548 bytes - dc.format.mimetype application/pdf - dc.relation (關聯) Genome Research, Vol.24, pp.2077-2089 dc.title (題名) Alignathon: A competitive assessment of whole genome alignment methods dc.type (資料類型) article dc.identifier.doi (DOI) 10.1101/gr.174920.114 dc.doi.uri (DOI) http://dx.doi.org/10.1101/gr.174920.114
