Note: This version is a preliminary draft. Comments and suggestions are welcome. Abstract Predicting gene structure requires search within a combinatorially large space of possible gene structures. The search space may be narrowed by two types of computational tools: optimality criteria and consistency constraints. Consistency constraints are requirements concerning reading frame and stop codon...

Substitution matrices are among the most widely used scoring techniques : BLAST, Muscle and other alignment packages, all use them. However these matrices are general; they ignore organism specific properties and do not provide customized scoring schemes. We present a Φhage-specific scoring matrix based on the abundances of aligned substitutions. These matrices use information from approximatel...

In this study, we present a pronunciation scoring method for second language learners of English (hereafter, L2 learners). This study presents a method using both confidence scoring and classifiers. Classifiers have an advantage over confidence scoring for specialization in the specific phonemes where L2 learners make frequent errors. Classifiers (Landmark-based Support Vector Machines) were tr...

performance optimization of chisel tine was proposed by using a chisel plow with adjustable rake angle. effective treatments consisted of soil moisture at 0.5, 0.7 and 0.9 of plastic limit (pl), three rake angle of 30, 40 and 50 degree and speeds of to 3, 5 and 7 km h-1. the measured parameters included draft, soil disturbance area, soil upheaving area, clod mean weight diameter (mwd), specific...

Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality...

Accurate scoring of protein-ligand interactions in molecular docking and virtual screening is still challenging. Despite great efforts, the performance of existing scoring functions strongly depends on the target structure under investigation. Recent developments in the direction of target-class-specific scoring methods and machine-learningbased classification models reveals a significant impro...