GDE
for Linux menu download:
Contents: HIV Sequence datasets, HIV Sequence
databases, Bioinformatics software,
References and Online resources
HIV-1 Sequence datasets
1. Reference sequence : HXB2
(9719bp) Complete genome,
FASTA file, GenBank file, Genome
picture
2. Genetic variants dataset: (extracted
from Los Alamos HIV Sequence DB)
Complete genome HIV-1/SIVcpz: FASTA file , file details.
Genome regions: gag, pol, vif, vpr, vpu, tat, rev, env, nef.
3. Dataset for phylogenetic analysis:
HIV-1 M group Complete genome (27 strains): FASTA file
HIV-1 M group Genome regions: gag,pol,vif,vpr,vpu, tat,rev,env,nef. (27 strains): FASTA
file
HIV-1 Subtype Complete genome (27 strains): FASTA file
HIV-1 Subtype C genome regions: gag,env (27 strains):
4. Others datasets (drug resistance, recombination,
etc.).
HIV-1 subtype A,B,C
and D protease function. (drugs biding sites, resistance mutations,
secondary structure, and CTL epitopes).
HIV-1 subtype A,B,C and D
Reverse Transcriptase function. (drugs biding sites, resistance
mutations, secondary structure, and CTL epitopes).
Sequence Databases for local BLAST and Xylem access:
1. Genbank database (68.000 sequences)
FASTA file
2. Database for genetic classification:
HIV-1 M group Complete genome (27 strains): FASTA file
3. Others databases (numbering positioning).
HXB2 (9719bp) Complete genome, FASTA
file,
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Software Integrated with
GDE linux:
A large number of software had been integrated, list of the software
The software need to be installed in your system following the instructions.
[PDF file]
Online Resources:
Sequence Databases:
Los Alamos HIV Sequence
Database Los Alamos National Laboratory, USA
Los Alamos Immunology Website, houses
a huge search able collection of HIV immunological epitopes
Los
Alamos Drug Resistance Database contains information about anti-HIV
drugs and drug-resistance-conferring mutations
 The HIVBase sequence database allow
the user to manage locally large number of sequences and clinical data
before publication
Retrovirus Resources at NCBI
Viral
Genome resource at NCBI
Stanford Drug
Resistance Database - Curated database containing RT and
Protease sequences for evolutionary and drug resistance studies.
SWISS-PROT
(amino acid sequences and others)
Entrez
(GeneBank+PIR+Medline) at NCBI
HIV-1 Taxonomy:
International
Committee on Taxonomy of Viruses
HIV
Taxonomy report NCBI
Alignments search and repositories:
HIV
Genomic Map at NCBI
HIV
Sequence search engine - Retrieve HIV sequences at Los Alamos
HIV
Sequence Db.
Online Programs:
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
Recombinant
Identification Program (RIP) - Los Alamos HIV Sequence Db.
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