A comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody.
A software for studying the physiology of immune-cell types in complex tissues on the basis of gene-expression data, without the need for experimental cell sorting. ImmQuant builds on the DCQ deconvolution algorithm and allows a user-friendly utilization of this method by non-bioinformatician researchers. Specifically, it enables investigation of hundreds of immune cell subsets in mouse tissues, as well as a few dozen cell types in human samples.
Identifies typical immunosuppressive domain (ISD) of retroviruses, including human endogenous retrovirus (HERV), human T-lymphotropic virus type 1 (HTLV-1), human immunodeficiency virus type 1 (HIV-1), simian T-lymphotropic virus (STLV) and simian immunodeficiency virus (SIV). ISDTool is a computational model that consists of two modules, ISDFindera for amino acid sequences and ISDFindern for DNA sequences.
Contains information on domain classes and homology blocks and classifies new sequences. VarDom facilitates the development of new approaches in PfEMP1 research and allows better interpretation. It permits to classify new sequences and relate it to other PfEMP1 proteins in seven genomes. The tool is applicable to any protein dataset, and is suitable for compositional analysis of other frequently recombining gene families.
Provides a R script of feature selection procedure. VallettaAndRecker2017 offers a random forests machine learning approach developed to analyse antibody profiles against panels of P. falciparum-specific antigens with the aim to identify signatures that are predictive of an individual’s protective status against clinical malaria episodes.
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