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BMCBI
2010

Towards realistic benchmarks for multiple alignments of non-coding sequences

13 years 11 months ago
Towards realistic benchmarks for multiple alignments of non-coding sequences
Background: With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based benchmarks have been proposed to meet this necessity, especially for non-coding sequences. However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks. Results: We find that the conventional simulation approach, which relies on empirically estimated values for various parameters such as substitution rate or insertion/deletion rates, is unable to generate synthetic sequences reflecting the broad genomic variation in conservation levels. We tackle this problem with a new method for simulating non-coding sequence evolution, by relying on genome-wide distributions of evolutionary parameters rather than their averages. We then generate synthetic data sets to mimic orthologous seque...
Jaebum Kim, Saurabh Sinha
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Jaebum Kim, Saurabh Sinha
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