TASK DEFINITION: In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
PROBLEM: We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ($3700 18-mers or $2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.

SOLUTION: Multiplex primer prediction software for divergent targets

PROBLEM: The emergence of the severe acute respiratory syndrome coronavirus (SARS-CoV) has led to a renewed interest in studying the role of accessory proteins in regulating coronavirus infections in the natural host. A significant body of evidence has accumulated in the area of SARS-CoV and host interactions that indicate that the accessory proteins might play an important role in modulating the host response to virus infection and thereby, contribute to pathogenesis. In this review, we have compiled the current knowledge about SARS-CoV accessory proteins, obtained from studies in cell culture systems, reverse genetics and animal models, to shed some light into the possible role of these proteins in the propagation and virulence of SARS-CoV in its natural host. We conclude by providing some questions for future studies that will greatly advance our knowledge about the biological significance and contributions of the accessory proteins in the development of SARS in humans.

SOLUTION: SARS coronavirus accessory proteins

PROBLEM: A novel coronavirus (SARS-CoV-2) is the causative agent of an emergent severe respiratory disease 20 in humans that is threatening to result in a global health crisis. By using genomic, sequence, 21 structural and evolutionary analysis, we show that Alpha-and Beta-CoVs possess several novel families 22 of immunoglobulin (Ig) domain proteins, including ORF8 and ORF7a from SARS-related coronaviruses 23 and two protein groups from certain Alpha-CoVs. Among them, ORF8 is distinguished in being rapidly 24 evolving, possessing a unique insert and a hypervariable position among SARS-CoV-2 genomes in its 25 predicted ligand-binding groove. We also uncover many Ig proteins from several metazoan viruses 26 which are distinct in sequence and structure but share an architecture comparable to that of CoV Ig 27 domain proteins. Hence, we propose that deployment of Ig domain proteins is a widely-used strategy by 28 viruses, and SARS-CoV-2 ORF8 is a potential pathogenicity factor which evolves rapidly to counter the 29 immune response and facilitate the transmission between hosts. 30 31

SOLUTION:
Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses