parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees参数和非参数随机性的掩蔽序列比对可以提高,带来更好的解析树.pdf

Kück et al. Frontiers in Zoology 2010, 7:10 /content/7/1/10 M E T H O D O L O G Y Open Access Methodology Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees 1 1 1 1 1 Patrick Kück* , Karen Meusemann , Johannes Dambach , Birthe Thormann , Björn M von Reumont , 1 2 Johann W Wägele and Bernhard Misof Abstract Background: Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. Results: ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both m