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I begin the chapter with a discussion of the fundamental principles of multiple-sequence alignment starting with pair-wise dynamic programming, then I move onto significance and similarity statistics, then amino acid scoring matrices, and I end the introduction with multiple-sequence alignment algorithms themselves. Reliability issues, complications, and applications of multiple-sequence alignment...
The Z-value (Comput. Chem. 23 (1999) 333) is an extension of the Z-score that is classically used to compare sets of biological sequences. The Z-value has been successfully used to handle complete genome studies as well as analyze large sets of proteins. The Z-value computation is based on a Monte Carlo approach to estimate the statistical significance of a Smith & Waterman alignment score. Comet...
The Z-value is an attempt to estimate the statistical significance of a Smith-Waterman dynamic alignment score (SW-score) through the use of a Monte-Carlo process. It partly reduces the bias induced by the composition and length of the sequences.This paper is not a theoretical study on the distribution of SW-scores and Z-values. Rather, it presents a statistical analysis of Z-values on large datasets...
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