BioAfrica - HIV Bioinformatics resources online

Search Sequence Databases:	HIV Specialized Databases:
Main Sequence databases (include DNA, RNA, protein and structure data) Entrez (GeneBank+PIR+Medline) at NCBI SRS7 (Sequence Retrieval System) at Sanger Centre - EMBL DDJB database from japan Patheways Search. KEEG - Pathway Information database Protein Databases: SWISS-PROT (amino acid sequences and others) PIR (Protein Identification Resource) (amino acid sequences and others) PDB (Protein Data Bank) (three-dimensional structures of proteins) Motif and Transcription Factors Databases: MOTIF - Dictionary of Protein Sites and Patterns PROSITE - Protein Motif Fingerprint Database Blocks Database - Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins ProDom - Protein domain database Vector-DB TRANSFAC - Transcription Factor Database AliBaba - Transcriptor factor Finder with graphical output	Los Alamos HIV Sequence Database Los Alamos National Laboratory, USA Los Alamos Immunology Website, houses a huge searchable collection of HIV immunological epitopes Los Alamos Drug Resistance Database contains information about anti-HIV drugs and drug-resistance-conferring mutations Retrovirus Resources at NCBI The HIVBase sequence database allow the user to manage locally large number of sequences and clinical data before publication. Stanford Drug Resistance Database - Curated database containing RT and Protease sequences for evolutionary and drug resistance studies. HIV Protease Database - Structural database maintained at the NCI devoted to HIV and SIV protease AIDS Reagent Program The NIH AIDS Research and Reference Reagent Program provides biological and chemical materials for study chemical materials for study of HIV and related opportunistic infections.
HIV Bioinformatics Tools Online:	HIV Sequence Database and Blast Search:
Gapstrip This tools lets you strip out the gaps from your sequences, in preparation for making a tree or other analysis. Multiple Motif Scan Search HXB2 or your own amino acid sequence for any HLA peptide binding motif Primalign Automatically align your primer or sequence fragment to the complete genome alignment. The interface returns the coordinates (HXB2 numbering) and an alignment of the fragment to all sequences in the whole genome alignment Epilign Automatically align your amino acid epitope against the alignments we have up on the web. SeqPublish Paste your alignment into the window and have it formatted for publication: identical columns are replaced by dashes, and the sequences are printed in blocks of user determined length. SIV/HIV locator tool at Los Alamos HIV Sequence Database. HXB2 Numbering Engine A quick way to find position numbers in HIV relative to HXB2. HIV Subtyping using BLAST This website allows subtyping of a new sequence by comparing it to a set of reference sequences using the BLAST local similarity search algorithm. HIV Subtyping analysis at Los Alamos Sequence Database SNAP (Synonymous/Non-synonymous Analysis Program) HYPERMUT This interface takes a nucleotide alignment and documents the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence.	BLAST searches for HIV, SIV, HCV and HBV at BioAfrica BLAST with microbial genomes at NCBI BLAST2 - NCBI HIV Blast at Los Alamos HIV Sequence Database Alignments: 2000 HIV and SIV alignments at Los Alamos HIV Sequence Database Subtype reference alignments at Los Alamos HIV Sequence Database . HIV Genomic Map at NCBI

The BioAfrica web site is maintained by: Dr. Tulio de Oliveira,