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2014 ; 30
(12
): i9-18
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Evaluating synteny for improved comparative studies
#MMPMID24932010
Ghiurcuta CG
; Moret BM
Bioinformatics
2014[Jun]; 30
(12
): i9-18
PMID24932010
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MOTIVATION: 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.
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