HIV sequence database
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ALIGNMENTS
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Index of all tools
ADRA
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Format converter
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HDent/HDdist
Heatmap
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Highlighter
HIV BLAST
HIValign
Hypermutation
jpHMM at GOBICS
Mosaic Vaccine
Tool Suite
Motif Scan
N-Glycosite
ODprep/ODfit
PCOORD
PeptGen
PhyloPlace
Primalign
Protein Feature
Accent
Protein structure
Recombinant HIV-1
drawing tool
RIP
SeqPublish
Sequence locator
SNAP
SUDI subtyping
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Sequence Search Interface
Tips
- Click or mouse over the field name for specific tips
- The
italicized fields
are listed in output by default
- To list fields that are not listed by default or included in the search, put an asterisk (*) in the input box
- For additional details about each field, see
Help
Last
GenBank
update: Sep 11 2008
Advanced Search
Sequence Information
Accession number
Subtype
Any
no subtype
A
A1
A2
B
C
D
F
F1
F2
G
H
J
K
N
O
U
CRF01_AE
CRF02_AG
CRF03_AB
CRF04_cpx
CRF05_DF
CRF06_cpx
CRF07_BC
CRF08_BC
CRF09_cpx
CRF10_CD
CRF11_cpx
CRF12_BF
CRF13_cpx
CRF14_BG
CRF15_01B
CRF16_A2D
CRF18_cpx
CRF19_cpx
CRF20_BG
CRF21_A2D
CRF22_01A1
CRF23_BG
CRF24_BG
CRF25_cpx
26_AU
CRF27_cpx
28_BF
29_BF
30_0206
31_BC
32_06A1
33_01B
34_01B
35_AD
36_cpx
37_cpx
38_BF
39_BF
40_BF
41_CD
42_BF
BABOON
COLOBUS
CPZ
DEBRAZZAS
DENT's
DRILL
GORILLA
GRIVET
GSN
LHOEST
MAC
MANDRIL-1
MANDRIL-2
MNE
MONA
MUSTACHED
MUSTACHED-1
MUSTACHED-2
PATAS
RCM
SABAEUS
SMM
STM
SUN
SYKES
TALAPOIN
TANTALUS
VERVET
Sequence name
Sampling country
Sampling city
Incl recombinants
Sampling year
Organism
Any
HIV-1
HIV-2
SIV
SHIV
Sequence length
Incl
problematic
seqs
yes
no
Patient Information
Patient code
Infection country
Risk factor
Any
list field in output
Heterosexual
Male sex with male
Non-sterile medical
Mother -> Child
IV Drug User
Sexworker
Experimental
Infection year
Viral load
Incl only sequences from patients with
HLA information
yes
no
CD4 count
CD8 count
Other Information
Coreceptor
list field in output
only CCR5
all CCR5
only CXCR4
all CXCR4
only R5X4
all R5X4
all CCR1
all CCR2B
all CCR3
all CCR8
all GPR1
all GPR15
all STRL33
all US28
all V28
Phenotype
list field in output
NSI
SI
Incl only
drug naive
sequences
yes
no
Author last name
Days from seroconversion
Geographic region
Any
list field in output
North America
South America
Central America
Caribbean
Oceania
Middle-East
Asia
Africa
Europe
Former USSR
Antarctica
Sub-saharan Africa
Days from infection
Pubmed/Medline ID
Other fields
Infection city
Title
Comment
Patient sex
Project
Progression
# of patient seqs
Patient age (days)
Patient health
Isolate name
Clone name
Sample tissue
Culture method
SE id
Find all sequences for a specific gene or region
Specific regions of
HIV-1
and
SIVcpz
can be retrieved from the HIV database using the following options:
Include fragments of minimum length
Genomic region
Any
complete genome
5' LTR
5' LTR R
5' LTR U3
5' LTR U5
TAR
Gag-Pol
Gag
p17 (matrix)
p24 (capsid)
p7 (nucleocapsid)
p6
Pol CDS
p51 (RT)
p15 (RNAse H)
p31 (integrase)
protease
Vif CDS
Vpr CDS
Tat CDS (plus intron)
Tat exon 1
Tat exon 2
Rev CDS (plus intron)
Rev exon 1
Rev exon 2
Vpu CDS
Env CDS
V1
V2
V3
V4
V5
RRE
gp41
gp120
Nef CDS
Or define
start
and
end
To retrieve HIV-1 sequences form the database and integrate them into your own sequence alignment, paste your
aligned
nucleotide sequences into the submission box below.
Or upload your
alignment
file:
Output
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records per page
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last modified: Thu Sep 4 07:34 2008
Questions
or
comments? Contact us at
seq-info@lanl.gov
.