Appendix.
Web Resources for HIV Drug Resistance Testing in Clinical and Research Settings
| Web address | Features | |
|---|---|---|
| Drug resistance data | ||
| Los Alamos National Laboratory HIV Sequence Database | http://hiv-web.lanl.gov | Searchable HIV-related data bases including a database of drug-resistance mutations. |
| Stanford HIV RT and Protease Sequence Database | http://hivdb.stanford.edu/hiv | A comprehensive database of HIV RT and protease sequences linked to treatment data and phenotypic drug susceptibility data |
| International AIDS Society-USA | http://hivinsite.ucsf.edu/ | Contains the most recently published guide lines (Hirsch et al., 2000) along with simplified diagrams of key drug resistance mutations. |
| Sequence analysis programs | ||
| PHYLIP | http://evolution.genetics.washington.edu/phylip.html | PHYLIP is a free, comprehensive package of programs for phylogenetic analysis of sequence data. This site also a comprehensive set of links to other sequence analysis tools. |
| IUBIO archive | http://iubio.bio.indiana.edu/soft/molbio/ | A comprehensive set of links to sequence analysis programs. |
| Los Alamos National Laboratory HIV Sequence Database | http://hiv-web.lanl.gov | Programs for making alignments and phylogenetic trees, estimating synonymous/nonsynonymous substitutions, detecting signature mutations and inter-subtype recombination. |
| Stanford HIV RT and Protease Sequence Database | http://hivdb.stanford.edu/hiv (link to http://hiv-4.stanford.edu/cgi-bin/hivseq-web.pl and http://hiv-4.stanford.edu/cgi-test/hivtest-web.pl) | Two programs including HIV-SEQ and a drug resistance interpretation program. The release notes for HIV-SEQ contain the consensus B protease and RT sequences. |
| BLAST | http://ncbi.nlm.nih.gov | Nucleotide and amino acid sequence similarity search |
| TreeView | http://taxonomy.zoology.gla.ac.uk/rod/treeview.html | Viewing and manipulating tree files |
| Suppliers of systems for HIV sequence analysis | ||
| Applied Biosystems | http://www.appliedbiosy-stems.com | ViroSeqTM HIV-1 Genotyping System, reagents and equipment for home-brew assays |
| Visible Genetics | http://www.visgen.com | TRUGENE TM HIV-1 Genotyping Kit, TRUPREPTM RNA isolation kit |
| Innogenetics | http://www.innogenetics.com | INNO-LiPA(R) HIV-1 line probe assays |
| Affymetrix | http://www.affymetrix.com | Affymetrix GeneChip(R) Systems |
| Companies that provide phenotypic assays | ||
| Virco, Inc. | http://www.vircolab.com | Services include the AntivirogramTM phenotyping assay, VirtualPhenotypeTM, and GENChecTM genotyping assay |
| ViroLogic | http://www.virologic.com | Services include the PhenoSenseTM phenotyping assay |