DistanceScan: a tool for promoter modeling

DistanceScan: a tool for promoter modeling

SUMMARY The state of the art in promoter modeling for higher eukaryotes is predicting not single transcription factor binding sites (TFBSs), but their combinations. The new tool utilizes a previously developed method of distance distributions of TFBS pairs. We model the random distribution of distances and compare it with the distribution observed in the query sequences. Comparison of the profi...

Application of Genetic Programming as a Powerful Tool for Modeling of Cellulose Acetate Membrane Preparation

A Petri-net based modeling tool, for analysis and evaluation of computer systems

Petri net is one of the most popular methods in modeling and evaluation of concurrent and event-based systems. Different tools have been created to support modeling and simulation of different extensions of Petri net in different applications. Each tool supports some extensions and some features. In this work a Petri net based modeling and evaluation tool is presented that not only supports dif...

A tool-kit for cDNA microarray and promoter analysis

We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. It allows combining of result files into comprehensive data sets, evaluation of the quality of both technical and biological replica...

Computer modeling of promoter organization as a tool to study transcriptional coregulation.

Understanding how the regulation of gene networks is orchestrated is an important challenge for characterizing complex biological processes. Gene transcription is regulated in part by nuclear factors that recognize short DNA sequence motifs, called transcription factor binding sites, in most cases located upstream of the gene coding sequence in promoter and enhancer regions. Genes expressed in ...