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Sequence Search Interface
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italicized fields
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Last
GenBank
update: 2024-02-14
Advanced Search
Sequence Information
Upload accession file
Accession number
Virus
Any
HIV-1
HIV-2
SIV
SHIV
synthetic DNA
NULL
Sequence name
Subtype
Sequence length
exact
Sampling year
Sampling country
Include
recombinants
More sequence information
Sequence id
GB create date(YYYY)
Isolate name
Clone name
Sample tissue
Any
list field in output
activated CD4+ T cells
adrenal gland
aorta
appendix
ascites
BAL
basal ganglia
blood
blood plasma; whole saliva
bone marrow
brain
breast milk
breast milk supernatant
carcinoma
CD14+ monocytes
CD16+ monocytes
CD3+ T cells
CD4 T cells
CD4+ T cells
CD4+ T cell supernatant
CD8+ T cells
central memory T cells
cervicovaginal secretions
cervix
choroid plexus
colon
CSF
culture supernatant
dendrites
diaphragm
duodenum
effector memory CD4+ T cells
effector memory T cells
epidermis
epididymis
esophagus
feces
foreskin
GALT
gastric aspirate
gastrointestinal tumor
glioma
heart
ileum
Ileum
intestine
jejunum
kidney
lamina propria mononuclear cells
liver
LN
lung
lymph node
lymph node CD4+ T cells
lymphocytes
lymphoma
meninges
monocyte
MT-2
MT4 cells
naive CD4+ T cells
ocular aqueous humor
pancreas
PBMC
PBMC supernatant
placenta
plasma
PMBC
prostate
prostatic secretion
qVOA
QVOA
rectal fluid
rectum
resting CD4+ T cells
saliva
semen
seminal cells
seminal plasma
seminal vesicle
serum
sigmoideum
skin lesion
skin tumor
spinal cord
spleen
sputum
stem memory T cells
stomach
supernatant
T-cell
T cells
terminally differentiated T cells
testes
testis
thymus
tonsil
transitional memory T cells
tumor
umbilical cord plasma
urethra
urine
urine cells
vagina
vaginal cells
vaginal fluid
vas deferens
whole blood
whole saliva
NULL
Culture method
Any
list field in output
primary
expanded
uncultured
unknown
NULL
Molecule type
Any
list field in output
DNA
mRNA
RNA
UNK
NULL
Amplification strategy
Any
list field in output
bulk
limiting dilution PCR
SGA
vector cloning
NULL
Sequencing method
Any
list field in output
clone
direct
NGS clone
NULL
Only
drug naive
sequences
Comment
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
Find all sequences for a specific gene or region (HIV-1, SIVcpz and SIVgor)
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
Include
fragments
of minimum length
Combine database sequences with your own sequence alignment (HIV-1, SIVcpz and SIVgor)
Selects a specific
genomic region
based on your input alignment.
Paste your
aligned
nucleotide sequences into the box:
Or upload your
alignment
file:
Use first sequence in alignment to define region
Use
ragged ends
to define region
Publication Information
Publication id
Author last name
PubMed id
Title
Journal
Patient Information
Patient id
Patient code
Risk factor
Any
list field in output
Heterosexual
Male sex with male
Sexual unspecified
Non-sterile medical
Mother->Child
IV Drug Use
Sex worker
Experimental
Sexual transmission, unspecified
Infection year
Only sequences with
HLA information
Patient sex
Any
list field in output
Female
Male
NULL
Days from seroconversion
Days from infection
Project
Any
list field in output
10-1074 Phase I trial
1182_12
1182_48
ACSR
ACTG
ACTG 229
ACTG 315
ACTG 359
ACTG 5077
ACTG 5211
ACTG 5241
ACTG A5095
ACTG A5142
ACTG A5197
ACTG A5197
AIEDRP
AIIMS cohort
ALIVE cohort
ALT ANRS
ANRS
ANRS PRIMO
ATCG
ATHENA
AVIP
Amsterdam Cohort Studies
Ariel
Australian LTNP Study
BEEHIVE
Belgian Transmission Chain
Bonn Cohort
Boston Acute Infection Cohort
Botswana Combination Prevention Project
Botswana-Harvard Partnership
CAPRISA
CAVD
CDC
CDC seroconversion cohort
CHAP2
CHAVI
CIPRA-SA
CNAB2006
CODE
Cato Manor
Copenhagen cohort
DMP266
Dakar FSW cohort
Danish HIV Cohort Study
EQAPOL
EQAPOL
EXPLORE
East London HIV-1 cohort
FCHC
FRESH
Frankfurt HIV cohort
French ALT Study Group
German Seroconverter Study
Good Health for Women Project
HISIS
HIV seroconverter cohort
HIV-STAR
HIVNET 006
HIVNET 012
HIVNET 023
HIVNET 028
HIVNET 028
HOMER
HPTN 033
HPTN 043
HPTN 046
HPTN 052
HPTN 058
HPTN 061
HPTN 068
HPTN 074
HPTN 078
HVTN
HVTN 502
HVTN 503
HVTN 505
IAVI
Italian Multicenter Mutations and Salvage Study
Italian Seroconversion Study
KiBS
Kumamoto University/NCGM Cohort (KI)
LAC-USC Rand Schrader Clinic
MACS
MAHS
MARCH
MGH cohort
MHP Cohort
MHRP
MOTIVATE
MRC
MUCOVIR
MUSH cohort
Mashi Study
Merck 035
Mochudi Prevention Project
Montreal Primary HIV Infection Cohort
Mortimer Market Centre
NAIAD
NIAID
NIBSC
NIH
NIH 15-I-0140 trial
NIH AVBIO cohort
NNAB
NVAZ
Nairobi cohort
New England Hemophilia Cohort
New York City Perinatal HIV Trial
OPTIONS
Opiate Users Research Study
PACTG P1022
PACTG P1030
PACTG P1059
PEPI-Malawi trial
PMTCT
PRIMO
Partners in Prevention Transmission Study
Phambili
Primo-SHM
Pumwani Majengo sex worker cohort
Quattro
RV121
RV126
RV144
RV217
RV254
RV254
RV397
RV405
RV411
RWISA
RZHRG
Ragon Institute
Rakai Community Cohort Study
Reduc Part B Trial
Rural Clinical Cohort
Rwanda Projet San Francisco
SCOPE
SFMHS
SIMBA
SPARTAC
SPREAD
STEP Trial
STI
SWEN Trial
San Francisco Mens Health Study
Seattle primary infection cohort
Sidney Blood Bank Cohort
Sinikithemba
South African National Blood Service
Stanford HIV Aging Cohort
Swiss HIV Cohort Study
Sydney Blood Bank Cohort
TRAPS
Trinidad and Tobago acute seroconverters
Tygerberg Virology Cohort
UAB
UARTO
UCLA Perinatal Transmission Study
UNC
UVRI
UW
Ugandan General Population Cohort
University of Pittsburgh Clinical Trials Unit
VAX003
VAX004
VRC 601
WHIS
WITS
Wadsworth Center
Western Australian HIV Cohort
Womens HIV Interdisciplinary Network
Womens Interagency HIV Study
ZEBS
ZEHRP
Zurich Primary HIV Infection Cohort
Patient health
Any
list field in output
acute infection
AIDS
asymptomatic
symptomatic
deceased
chronic
treatment failure
NULL
Fiebig stage
Vaccine status
Any
list field in output
preventative placebo
preventative breakthrough
placebo
therapeutic pre-treatment
therapeutic post-treatment
NULL
More patient information
Patient age
Viral load
CD4 count
CD8 count
Progression
Any
list field in output
elite controller
long-term non-progressor
slow progressor
rapid progressor
progressor
NULL
# of patient seqs
# of patient timepoints
Cluster transmission type
Any
list field in output
Mother->Child
Non-sterile medical
Not recorded
Other
IV Drug Use
Heterosexual
Male sex with male
Sexual unspecified
Cluster name
Cluster comment
Geographical Information
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
Sampling city
Infection country
Infection city
Amino Acid Motif Search
Motif
Gene
Any
list field in output
Env
Gag
Nef
Pol
Rev
Tat
Vif
Vpr
Vpu
Vpx
Output
Include
problematic
sequences
% of non-ACGT
List
records per page
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Advanced Search
last modified: Tue May 23 09:03 2023
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