Pathogen Sequence Signature Analysis (PSSA): A software tool for analyzing sequences to identify microorganism genotypes

VIRALpro: a tool to identify viral capsid and tail sequences

MOTIVATION Not only sequence data continue to outpace annotation information, but also the problem is further exacerbated when organisms are underrepresented in the annotation databases. This is the case with non-human-pathogenic viruses which occur frequently in metagenomic projects. Thus, there is a need for tools capable of detecting and classifying viral sequences. RESULTS We describe VIR...

Using A Taxonomy Tool To Identify Changes in OO Software

In this paper, we present a taxonomy that allows the maintainer to catalog OO classes based on the characteristics of the class. The characteristics of a class include the properties of data items and methods, as well as the relationships with other classes in the application. We construct a tool to track changes across multiple releases of software applications containing hundreds of classes, ...

CodonShuffle: a tool for generating and analyzing synonymously mutated sequences

Because synonymous mutations do not change the amino acid sequence of a protein, they are generally considered to be selectively neutral. Empiric data suggest, however, that a significant fraction of viral mutational fitness effects may be attributable to synonymous mutation. Bias in synonymous codon usage in viruses may result from selection for translational efficiency, mutational bias, base ...

Dna Sequence Analysis: the Development of a Custom Software Tool

A Neural Network Based Security Tool for Analyzing Software

The need to secure software application in today’s hostile computer environment cannot be overlooked. The increase in attacks aimed at software directly in the last decade and the demand for more secure software applications has drawn the attention of the software industry into looking for better ways in which software can be developed more securely. To achieve this, it has been suggested that ...