000203637 001__ 203637
000203637 005__ 20190522142440.0
000203637 0247_ $$2doi$$a10.1093/bioinformatics/btu259
000203637 022__ $$a1367-4803
000203637 02470 $$2ISI$$a000338109200002
000203637 037__ $$aCONF
000203637 245__ $$aEvaluating synteny for improved comparative studies
000203637 269__ $$a2014
000203637 260__ $$bOxford University Press$$c2014
000203637 336__ $$aConference Papers
000203637 500__ $$aNational Licences
000203637 520__ $$aMotivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected-what few results are given use superficial measures unrelated to quality or consistency. Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles.
000203637 542__ $$fCC BY-NC
000203637 700__ $$aGhiurcuta, Cristina G.
000203637 700__ $$g172233$$0241987$$aMoret, Bernard M. E.
000203637 7112_ $$aIntelligent Systems for Molecular Biology ISMB'14
000203637 773__ $$j30$$tBioinformatics$$k12$$q9-18
000203637 8564_ $$uhttps://infoscience.epfl.ch/record/203637/files/btu259.pdf$$zPUBLISHER'S VERSION$$s703947
000203637 909C0 $$xU11274$$0252020$$pLCBB
000203637 909CO $$pconf$$pIC$$ooai:infoscience.tind.io:203637
000203637 917Z8 $$x148230
000203637 937__ $$aEPFL-CONF-203637
000203637 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000203637 980__ $$aCONF