All Sequence and Code Analysis Algorithms

Algorithms that analyze sequences of symbols, whether the letters of a DNA or RNA molecule or the codewords of a code. The Nussinov algorithm predicts the folding of an RNA molecule using dynamic programming, the Shapiro-Senapathy algorithm scores sequences with a position weight matrix to identify splice sites in genes, the Z curve method represents a DNA sequence uniquely as a three-dimensional curve for genome analysis, and the Sardinas-Patterson algorithm determines in polynomial time whether a variable-length code is uniquely decodable. An algorithm belongs here when its cited article describes analyzing or predicting properties of a symbol sequence such as a nucleic acid sequence or a code. It excludes general methods for aligning or comparing sequences, which belong with the edit distance and sequence alignment algorithms, and methods that make data smaller, which belong with the data compression algorithms.