Functional Microbial Genomics...HIV Shainn-Wei Wang,Ph.D. NCKU,College of Medicine Institute of Molecular Medicine
Functional Microbial Genomics…HIV Shainn-Wei Wang, Ph.D. NCKU, College of Medicine Institute of Molecular Medicine
HIV exhibits tremendous genetic diversity Global influenza 1996 Congo 1997 HIV single individual 6 years after infection HIV Amsterdam cohort 1991 CRFO1 10% Garber D.A.,et al.,Lancet Infec.Dis.,2004
Garber D. A., et al., Lancet Infec. Dis., 2004 HIV exhibits tremendous genetic diversity
Los Alamos HIV Data Base NATIONAL LABORATORY http://ww.hiv.lanl.gov/content/index
HIV Data Base • http://www.hiv.lanl.gov/content/index
HIV/HCV Database http://lasp.cpqgm.fiocruz.br/Lasplngles/ferramentas.html Goncl Monlz Advanced Laboratory Research Center Biois of Public Healt FIOCRUZ-B3h怕 (LASP Home Bioinformatics Unit Tools Retrovirus Sequences HSat的inl Training and Courses LASP Info ad ara o Biftiso ·0 o Bimprom
http://lasp.cpqgm.fiocruz.br/LaspIngles/ferramentas.html HIV/HCV Database
Sequence Database: Entrez (GeneBank+PIR+Medline)on NCBI SRS7(Sequence Retrieval System)on Sanger Centre-EMBL SWISS-PROT (protein Data Base). PDB (Protein Data Bank)(3D structure Data Base). HIV Sequence Database: Los Alamos HIV Sequence Database HIV Data base) Stanford Drug Resistance Database Data Base of Reverse Transcriptase and Protease gene related to drug resistance). Retrovirus Resources (Data base and bioinformatics tool for retrovirus at NCBD). AIDS Reagent Program (Information about reagents used in HIV/SIDA research) HCV Sequence Data Base: Los Alamos HCV Sequence Database (HCV Data Base) The Japanese Hepatitis C Database (HCV Data Base) The French Hepatitis C Database (HCV Data Base) HTLV sequence Data Base:alignnent produced at (LASP/CPqGM/FIOCRUZ)
Bioinformatics tools for HIV sequence analysis NEw Subtyping Tool(Subtiyping program recently developed by the consultant of the Bioinformatics laboratory from LASP/FIOCRUZ). SIV/HIV locator tool Locates HIV genetic region) HIV Blast at LASP HIV Blast at BioAfrica HYPERMUT (locates hyper -mutations) HⅡV Sequence alignment: HIV and SIV alignments Los Alamos). Subtype reference alignments Los Alamos) Alignment at BioAfrica. Alignment at LASP Bioinformatics tools for HCV sequence analysis: HCV locator tool Locates HCV genetic region). HCV Blast at Los Alamos HCV Blast at BioAfrica. HCVPrimer Aligner (HCV Primer alignment) HCV sequence alignment: HCV reference alignments (Los Alamos)
址四a-o http://www.flu.lanl.gov/ The Influenza Sequence Database Home Search Vaccine SelectioReviews LinksContac Us Help Report aBugLogin About the ISD Welcome to the Influenza Sequence Database. Then Sene Database (S)a oubishedhc have ben You have several options for using the ISD cratedbyoostdadsof araydDormgof Cost Services rhienailseqpetcesandstdofthemoleculkr ewohthouoftheinhuenainsacedesigedtoemedtethe Access to al curated,public data typicadtasksofmolecularepidemolog.Stdbscripiosto Dowod ofmodratefata Free theISDaterequredfrfilaccesstotolk,mfomaionoi AcstoVacine Sele adother Revew the purhasefbbedy angov ·Alfthe above,pl咖s Subsp Altosuhs BLASTrfphyog Log to the database ·All of the above,pls ·Abi的tostorepvate da Work-for-thers ·Ab面to save workng set的 Aboheataer
http://www.flu.lanl.gov/
t四目-wa如go The Influenza Sequence Database Home Search Vaccine Selection Reviews Links Contact Us Help Report a Bug Logir Search Search Search Search F Species:☐A☐B☐C Any Segment Any Host Search Refine ☐NOT Any of n AFields Help Display Options per page Analysis and Tools Download Results
HIV Databases The HiV databases contain data on HiV genetic sequences,immunological epitopes,drug resistance-associated mutations,and vaccine trials.The website also aives access to a large number of tools that can be used to analyze these data.This project is funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases (NIAID).a part of the National Institutes of Health(NIH).Click on any of the links below to access a database Sequence Database Resistance Database Immunology Database Vaccine Trials Database HCV Databases news .A new tool to get colored overviews of alignments has been developed This tool,Highlighter,lets you label mismatches or matches to multiple master sequences as well as resort the sequences.The mismatches can be considered as all mismatches,transition/transversions or silent substitutions.The program allows IUPAC multistate characters.13 July 2006 .The Immune Epitope Database (IEDB)is available online.The IEDB is a project hosted at the La Jolla Institute for Allergy and Immunology(LIAl)that contains antibody and T cell epitope data curated from scientific literature and submitted from the community.as well as immunological analysis tools. 15May2006 Updated 2004 Web Alignments are now available on-line.The web alignments contain sequences received by the database up to and including 2004.27 April 2006
About this website: ·Overview of the site Frequently asked questions Programs and tools: Search interface:retriee qu basedll HIV database searh fields.HIV-1q be aliged and clipped.Neighbor-joining rc befo the guery results. conversion,N-GlycoSite,Entropy Programs for sequence analysis:RIP (Recombination),SNAP (Syn-Nonsyn),VESPA (Signature pattems),Hypermut,PCOORD,and more.. eorofHMAat怕a0 picda地 Tutorials: Sequence quality control Jaary19 How to build a phylogenetic tree1 Howodatabaseopt1th ConferenceRetr and pprisifection Alignments: Complete alignments of all genes (nt and aa)and complete genomes (nt only) Subtype referenc ComeadAnetrafoMP Compendia: Print (PDF)or order a copy of our annual compendium" Reviews published in the Sequence and mmooCompendia Howorfer to the ompendia in a publication Links: LoAmoeouretoa hucfHiop abase con anti HIV gesistancecoteringmtatoas