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...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Jaebum Kim, Saurabh Sinha
• Keywords: Alignment Task, BMCBI 2010, Non-coding Sequences, Tools