weight matrix (PWM) is often used to search for putative transcription factor binding sites. A set of experimentally verified oligonucleotides known to be functional motifs are collected and aligned. The frequency of each nucleotide A, C, G, or T at each column of the alignment is calculated in the matrix. Once a PWM is constructed, it can be used to search from a nucleotide sequence for subseq...

We continue our earlier investigation of properties of linear codes generated by the rows of incidence matrices of k-regular connected graphs on n vertices. The notion of edge connectivity is used to show that, for a wide range of such graphs, the p-ary code, for all primes p, from an n × 12nk incidence matrix has dimension n or n− 1, minimum weight k, the minimum words are the scalar multiples...

Protein sequence alignmentmay be viewed as either a classification or amultiple hypothesis testing problem.Whereas the type one error of a method is often studied for randomly generated sequences, the power is best investigated based on real protein sequences. The SCOP data base and its protein classification is used to investigate both the power and the type one error of sequence alignment as ...

During electroplating or heat treatment operations parts are usually mounted on plating or charging racks, which can for practical purposes be described as position matrices. An optimized production process should exhibit no significant changes in the quality characteristics of the products after going through the production cycle regardless of the product's position within the matrix. Measurem...