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
Sequence name
Sampling country
Sampling city	Incl recombinants
Sampling year	Organism
Sequence length	Incl problematic seqs	yes no
Patient Information
Patient code	Infection country
Risk factor	Infection year
Viral load	Incl only sequences from patients with HLA information	yes no
CD4 count	CD8 count
Other Information
Coreceptor	Phenotype
	Incl only drug naive sequences	yes no
Author last name	Days from seroconversion
Geographic region	Days from infection
Pubmed/Medline 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	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
List records per page
Show results selected
Advanced Search

last modified: Thu Sep 4 07:34 2008

Index of all tools	ADRA
Branchlength	Codon Alignment
Consensus Maker	ELF
ElimDupes	Entropy
Epilign	FindModel
Format converter	Gap strip/squeeze
Gene Cutter	HDent/HDdist
Heatmap	Hepitope
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	SynchAlign
Translate	Treemaker
External tools

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

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