The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback-Leibler divergence from the mean amino acid content as a metric to compare the amino acid composition for a large set of bacterial and phage genome sequences. Using these data, we demonstrate that (i) there is a significant difference between amino acid utilization in different phylogenetic groups of bacteria and phages; (ii) many of the bacteria with the most skewed amino acid utilization profiles, or the bacteria that host phages with the most skewed profiles, are endosymbionts or parasites; (iii) the skews in the distribution are not restricted to certain metabolic processes but are common across all bacterial genomic subsystems; (iv) amino acid utilization profiles strongly correlate with GC content in bacterial genomes but very weakly correlate with the G+C percent in phage genomes. These findings might be exploited to distinguish coding from non-coding sequences in large data sets, such as metagenomic sequence libraries, to help in prioritizing subsequent analyses.

{This paper presents a knowledge representation object language (KROL) on top of Prolog. KROL is aimed at providing the ability to develop second-generation expert systems. The main aspects of KROL include multi-paradigm knowledge representation (first-order predicate logic, objects, rules), inference mechanisms at different levels of granularity, explanation facility, object-oriented database management module, and user-friendly interface. KROL has sufficient expressive power to be used in applying demanding knowledge-based modeling methodologies, such as KADS and Generic Task, which are the major landmarks of the second-generation expert systems technology. Four successful agricultural expert systems have been developed in the last 6 years using KROL. To demonstrate the language capabilities, we present an example of disorder diagnosis.}

The maturity of Knowledge Engineering (KE) theory and practice presents a real opportunity for advancing the state-of-the-art and state-of-the-practice in software Product-line Engineering (PLE). Several challenges that face the adoption and implementation of PLE in practice can be addressed by exploiting advanced technique from KE. This paper introduces the concept of KOPLE and describes the related one-day workshop that will be held in conjunction with SPLASH 2010.