HIV Databases. HIV Molecular Immunology Database. HIV Molecular Immunology Database: Tools & Links. Hepitope: HLA-Enriched Possible Epitope. The Hepitope tool searches for hopeful-epitopes or "Hepitopes". The tool tests for HLA alleles that are enriched in a set of individuals that react with a set of peptides. This can be used in conjunction with ELF (Epitope Location Finder) to scan the peptides for known epitopes in the database and anchor motifs to help identify epitopes within a larger peptide fragment. See below for details about the input and output of the program. Input To look for HLA enrichment in reactive individuals, we just do a 2 by 2 contingency table.
We present four columns of data: a The number of individuals that carry the HLA allele and react with the peptide b The number of individuals that do not carry the HLA allele and react with the peptide c The number of individuals that carry the HLA allele and do not react with the peptide d The number of individuals that do not carry the HLA allele and do not react with the peptide The input requires two files: And so on for each peptide entered. ELF epitope location finder. HIV HLA Anchor Residue Motifs (Motif Scan) QuickAlign. HIV sequence database main page. HIV Database Tools Page. Sequence Alignments. Web Alignments are nucleotide and protein alignments that represent the fullest spectrum of sequences in the database.
Filtered Web Alignments are a filtered subset of sequences from the web alignments. These alignments are cleaner, but contain slightly less information. Subtype Reference Alignments contain approximately 4 representatives of each subtype. Compendium Alignments are the subset of sequences printed in the HIV Sequence Compendium. Consensus/Ancestral Sequences include a consensus for each subtype, an M-group consensus-of-consensuses, and some ancestral sequences. RIP Alignment contains a consensus for each subtype and reference sequences for all groups, subtypes, and CRFs. Javascript required This tool depends upon Javascript for its interactive features. . * “2008” alignments contains sequences published before 2009. ** User-defined ranges are clipped from a genome alignment. Web Alignments What sequences are included Only one sequence per patient is included. HIV Sequence Database: Entropy-One Submission Form. KEGG - Table of Contents.
KEGG PATHWAY Database. Antigen processing and presentation - Homo sapiens (human) Toll-like receptor signaling pathway - Homo sapiens (human) ONLINE ANALYSIS TOOLS. Alignments. PRALINE - is a multiple sequence alignment program with many options to optimize the information for each of the input sequences; e.g. global or local preprocessing, predicted secondary structure information and iteration capabilities. (Reference: V.A. Simossis et al. (2005) Nucleic Acids Res. 33: 816-824). A similar type of output can be obtained using SPEM (Laboratory of Biophysics & Bioinformatics, University of Buffalo, U.S.A.). Example of PRALINE output: Gene Context Tool - is an incredible tool for visualizing the genome context of a gene or group of genes (synteny).
In the following diagram an RpoN (Sigma54) protein was analyzed. (Reference: R. CARNA is a tool for multiple alignment of RNA molecules. IBIVU Server - PRALINE Multiple Sequence Alignment. Gene. European Bioinformatics Institute | Homepage. National Center for Biotechnology Information. Home - SNP - NCBI. NCBI Structure Group Home Page. Macromolecular Structures Resource Group. ExPASy: SIB Bioinformatics Resource Portal - Home.