jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach proposed by Spang et al.

Heterogeneity of papillomaviruses.

The classification of the papillomaviral sequence into types is satisfactory for many purposes, but the resulting catalog does not accurately depict the extent of diversification of this family of viruses. Phylogenetic and mutational analyses reveal that some viral forms are much more ancient than other forms. Episodic evolutionary events and zoonotic transmission may have contributed to the overall pattern.

The Human Papillomavirus Database.

Papillomaviruses are responsible for a variety of diseases in humans and animals, ranging from harmless skin warts to lethal cancers. They also make up one of the most genetically diversified families of viruses known, and could represent a model system of DNA-virus evolution. A specialized genetic sequences database, The Human Papillomavirus Database and Analysis Project, was recently established in an effort to provide database services that are specific to papillomaviruses to the research community and to perform a variety of sequence-based analyses.