WSE, a new sequence distance measure based on word frequencies

Oligo-distance: a Sequence Distance Determined by Word Frequencies

Differences in the frequencies of chemical words of a given length in two nucleic sequences are used to define an “oligo-distance” between the sequences. Oligo-distances are much easier and faster to compute than the distances conventionally determined by sequence alignment. A correlation between oligo-distance and alignment-distance is observed. The two kinds of distances are used to construct...

Some properties of a new fuzzy distance measure

A new distance measure for comparing sequence profiles based on path lengths along an entropy surface

We describe a new distance measure for comparing DNA sequence profiles. For this measure, columns in a multiple alignment are treated as character frequency vectors (sum of the frequencies equal to one). The distance between two vectors is based on minimum path length along an entropy surface. Path length is estimated using a random graph generated on the entropy surface and Dijkstra's algorith...

A new sequence distance measure for phylogenetic tree construction

MOTIVATION Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences...

K Modes Clustering Algorithm Based on a New Distance Measure

T he leading par tit ional clustering technique, K Modes, is one of the most computationally eff icient clustering methods fo r categ orical data. In the t raditional K Modes algo rithm, the simple matching dissim ilarity measure is used to compute the distance betw een two values of the same catego rical at t ributes. T his compares tw o categorical v alues directly and results in either a dif...