MOTIVATION: Swine leukocyte antigens (SLAs) (i.e. swine major histocompatibility complex proteins) conduct a fundamental role in swine immunity. To generate a protective vaccine across an outbred species, such as pigs, it is critical that epitopes that bind to diverse SLA alleles are used in the vaccine development process. We introduced a new strategy for epitope prediction. RESULTS: We employed molecular dynamics simulation to identify key amino acids for interactions with epitopes. We developed an algorithm wherein each SLA-1 is compared to a crystalized reference allele with unique weighting for non-conserved amino acids based on R group and position. We then performed homology modeling and electrostatic contact mapping to visualize how relatively small changes in sequences impacted the charge distribution in the binding site. We selected eight diverse SLA-1 alleles and performed homology modeling followed, by protein-peptide docking and binding affinity analyses, to identify porcine reproductive and respiratory syndrome virus matrix protein epitopes that bind with high affinity to these alleles. We also performed docking analysis on the epitopes identified as strong binders using NetMHCpan 4.1. Epitopes predicted to bind to our eight SLA-1 alleles had equivalent or higher energetic interactions than those predicted to bind to the NetMHCpan 4.1 allele repertoire. This approach of selecting diverse SLA-1 alleles, followed by homology modeling, and docking simulations, can be used as a novel strategy for epitope prediction that complements other available tools and is especially useful when available tools do not offer a prediction for SLAs/major histocompatibility complex. AVAILABILITY AND IMPLEMENTATION: The data underlying this article are available in the online Supplementary Material.

A software system evolves over time in order to meet the needs of users. Understanding a program is the most important step to apply new requirements. Clustering techniques through dividing a program into small and meaningful parts make it possible to understand the program. In general, clustering algorithms are classified into two categories: hierarchical and non-hierarchical algorithms (such as search-based approaches). While clustering problems generally tend to be NP-hard, search-based algorithms produce acceptable clustering and have time and space constraints and hence they are inefficient in large-scale software systems. Most algorithms which currently used in software clustering fields do not scale well when applied to large and very large applications. In this paper, we present a new and fast clustering algorithm, FCA, that can overcome space and time constraints of existing algorithms by performing operations on the dependency matrix and extracting other matrices based on a set of features. The experimental results on ten small-sized applications, ten folders with different functionalities from Mozilla Firefox, a large-sized application (namely ITK), and a very large-sized application (namely Chromium) demonstrate that the proposed algorithm achieves higher quality modularization compared with hierarchical algorithms. It can also compete with search-based algorithms and a clustering algorithm based on subsystem patterns. But the running time of the proposed algorithm is much shorter than that of the hierarchical and non-hierarchical algorithms. The source code of the proposed algorithm can be accessed athttps://github.com/SoftwareMaintenanceLab.