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damlab
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HIV_V3_bodysite

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train · 5.45k rows

sequence stringlengths 21 57	id stringlengths 6 8	fold int32 0 4	periphery-tcell bool 2 classes	periphery-monocyte bool 2 classes	CNS bool 2 classes	breast-milk bool 2 classes	female-genitals bool 2 classes	male-genitals bool 2 classes	gastric bool 2 classes	lung bool 2 classes	organ bool 2 classes
*TRPNNNTRKSIPMGPGRAFYTTGQITGDIRQAHC	Z34434	2	false	false	false	false	false	false	false	false	true
CAGPNNNTRRSINIGPGRAWYAIGDIIGDIRKAHC	JN856514	2	false	false	false	false	true	false	false	false	false
CAQDPPTQYKKGVYMDQGEQFIQRTKQEI*DKHI	U16061	1	false	false	true	false	false	false	false	false	false
CARASTNTRQSFHIGPGRAFYATGALLGDFCPAYC	U16052	1	false	false	true	false	false	false	false	false	false
CARLGNNTRKSVRIGPGQTFYATGDIIGDIRQAHC	KC187508	0	false	false	true	false	false	false	false	false	false
CARPANNTRTSVRIGPGQTFYATGEIIGNIREAHC	HM070605	4	true	false	false	true	false	false	false	false	false
CARPANNTRXSIRIGPGQTFYATGDIXGDIRQAHC	MH758639	4	true	false	false	false	false	false	false	false	false
CARPGNNTRKGIHIGPGRAFYATEDIVGDIRKAHC	HQ451263	4	true	false	false	false	false	false	true	false	false
CARPGNNTRKGIHMGPGGAFYTRGDIIGDIRQAHC	MH060211	0	true	false	false	false	false	false	false	false	false
CARPGNNTRKGIHMGPGRAFYTTGIVGDIRRAHC	JN407665	1	true	false	false	false	false	false	false	false	false
CARPGNNTRKGIRIGPGQTFFATGEIIGDIRQAHC	KP261392	1	false	false	false	true	false	false	false	false	false
CARPGNNTRKSIHIGPGRAFYATEDIIGDIRKAHC	HQ451270	4	false	false	false	false	false	false	true	false	false
CARPGNNTRKSIHIGPGRAFYATEVIGDIRKAHC	HQ451265	4	false	false	false	false	false	false	true	false	false
CARPGNNTRKSIPMGPGRAWFATGDIIGDIRQAHC	AF535521	4	false	false	false	false	false	true	false	false	false
CARPGNNTRKSIRIGPGQTFFATGEIIGDIRQAHC	KP261393	3	true	false	false	true	false	false	false	false	false
CARPGNNTRKSMRIGPGQTFYATGAIIGDIRQAHC	EU166576	3	true	false	false	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQAFFATNEIIGDIRQAHC	KY825630	1	true	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQAFFATNKIIGDIRQAHC	KY825633	4	false	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQAFYATGDVIGNIRQASC	MT347681	0	true	false	false	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFFAKGDIIGDIRQAHC	KC187109	4	false	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFFAKGDIIGNIRQAHC	KC187107	3	false	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFFANEDIIGDIRQAHC	KC187116	4	false	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFFANEDIIGNIRQAHC	KC187113	1	false	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFFANGDIIGDIRQAHC	KC187108	0	true	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFYATGDIIGDIRQAHC	KC187499	1	true	false	true	false	true	false	false	false	false
CARPGNNTRKSVRIGPGQTFYATGDIIGNIRQAHC	KC187511	2	false	false	true	false	false	false	false	false	false
CARPGNNTRKSVRIGPGQTFYATGEIIGDIRKAYC	HQ172377	0	false	false	false	true	false	false	false	false	false
CARPGNNTRKSVRIGPGQVFFANGDIIGDIRQAHC	KC187122	4	false	false	true	false	false	false	false	false	false
CARPGNNTRQSVRIGPGQTFYATGDIIGNPRVAHC	HM036829	3	true	false	false	false	false	false	false	false	false
CARPGNNTRRSIRIGPGQSFYATGEIIGDIRQAHC	KF374052	1	true	false	false	false	false	false	false	false	false
CARPGNNTRRSIRIGPGQTFFATGEIIGDIRQAHC	KP261418	0	false	false	false	true	false	false	false	false	false
CARPGNNTRRSVRIGPGQTFFANGDIIGDIRQAHC	KC187110	3	true	false	true	false	false	false	false	false	false
CARPGNNTRTSVRIGPGQTFYATGDIIGDIRKAHC	MF284955	4	false	false	true	false	false	false	false	false	false
CARPGSNTRKSIRIGPGQTFFATGEIIGDIRQAHC	KP261416	1	false	false	false	true	false	false	false	false	false
CARPHNNTRKSIPIGPGRAFYATGDITGDIRQAHC	HM638512	3	false	false	false	false	false	true	false	false	false
CARPNNNIRKSINIGPGRAFYAAGQIIGDIRQAHC	GU597225	2	false	false	false	false	false	true	false	false	false
CARPNNNKRKSIPIGPGRAFYATGDIIGDIREAYC	AF401331	2	true	false	false	false	false	false	false	false	false
CARPNNNTRDSIHMGPGKAFYTTGDIIGDIRQAHC	JN786693	4	false	false	false	false	false	false	false	false	true
CARPNNNTRDSIHMGPGKAFYTTGDIIGDIRQAHR	JN786702	0	false	false	false	false	false	false	false	false	true
CARPNNNTRDSIHMGPGKAFYTTGDIIGDIRQAHY	JN786699	0	false	false	false	false	false	false	false	false	true
CARPNNNTRDSIHMGPGKAFYTTGGIIGDIRQAHC	JN786720	4	false	false	false	false	false	false	false	false	true
CARPNNNTRKGIHIGPGGAFYTTGQIIGDIRQAHC	GQ456464	0	true	false	false	false	false	false	false	true	false
CARPNNNTRKGIHIGPGRAFYATGEIIGDIRQAHC	GQ456435	3	true	false	false	false	false	false	false	true	false
CARPNNNTRKGIHIGPGRAFYTTGQIIGDIRQAHC	GQ456462	0	true	false	false	false	false	false	false	true	false
CARPNNNTRKGIHIGPGRXFYATGDIIGDIRQAHC	AJ278204	1	true	false	false	false	false	false	false	false	false
CARPNNNTRKGIHIGPGSAFYATGDIIGDIRQAHC	JN786750	4	false	false	false	false	false	false	false	false	true
CARPNNNTRKGIHIGPGSAFYATGEIIGDIRQAHC	GQ456427	3	true	false	false	false	false	false	false	true	false
CARPNNNTRKGIHIGPGSAFYATGEIIGNIRQAHC	GQ456438	4	true	false	false	false	false	false	false	true	false
CARPNNNTRKGIHIRPKKTLYATEDIIRKIRQAHC	GU063517	0	false	true	false	false	false	false	false	false	false
CARPNNNTRKGIHMGPGRAMYATEKITGDIRQAHC	AY842826	4	false	false	true	false	false	false	false	false	false
CARPNNNTRKGIHVGPGGALYTTGQIIGNIRQAHC	GQ456557	4	false	false	false	false	false	false	false	true	false
CARPNNNTRKGIQIGPGRAFYATGEIIGDIRQAHC	GQ456437	2	true	false	false	false	false	false	false	true	false
CARPNNNTRKGIYIGPGRAVYARQKIIGDIRKAYC	HQ451840	3	false	false	false	false	false	false	true	false	false
CARPNNNTRKGMRIGPGQTFYATKDIIGDIRQAHC	HM036743	4	true	false	false	true	false	false	false	false	false
CARPNNNTRKGMRIGPGQTFYATKDIIGNIRQAHC	HM036740	1	false	false	false	true	false	false	false	false	false
CARPNNNTRKRIYMGTGRYMSATEKITGDIRQAHC	AY842825	2	true	false	true	false	false	false	false	false	false
CARPNNNTRKRIYMGTGRYMSATEKITGDIRQARC	AY842833	0	false	false	true	false	false	false	false	false	false
CARPNNNTRKSIHIGPGRAFYATGEIIGDIRKAHC	GU206647	0	true	false	true	false	false	false	false	false	false
CARPNNNTRKSIHIGPGRAFYTTGAIIGDIRQAHC	AF535287	1	false	false	false	false	false	true	false	false	false
CARPNNNTRKSIHIGPGRAFYTTGQIIGDIRQAYC	AF409639	4	false	false	false	false	false	false	false	false	true
CARPNNNTRKSIHIGPGRSFYATDIIGDIRQAHC	AY364685	2	true	false	false	false	false	false	false	false	false
CARPNNNTRKSIHIGPGRSFYTTGAIIGDIREAHC	LC326441	3	true	false	false	false	false	false	false	false	false
CARPNNNTRKSIHIGWGRAFYATGEIIGDIRQAHC	KF247120	2	true	false	false	false	false	false	false	false	false
CARPNNNTRKSIHIRPKKTLYATEDIIRKIRQAHC	GU063516	3	false	true	false	false	false	false	false	false	false
CARPNNNTRKSIHLGPGGAFYATGDIIGDIRQAHC	DQ976402	2	false	false	false	false	false	false	false	false	true
CARPNNNTRKSIHMGPGQALYATGNIIGDIRQAHC	KM259118	0	false	false	true	false	false	false	false	false	false
CARPNNNTRKSINIGPGGAWYATGEIIGDIRKAHC	JN856516	4	false	false	false	false	true	false	false	false	false
CARPNNNTRKSINIGPGRAFYAAGQIIGDIRQAHC	GU597226	4	false	false	false	false	false	true	false	false	false
CARPNNNTRKSINIGPGRAFYAAGQIVGDIRQAHC	GU597224	4	false	false	false	false	false	true	false	false	false
CARPNNNTRKSINIGPGRAFYATGDIIGNIRQAHC	KM353807	3	true	false	true	false	false	false	false	false	false
CARPNNNTRKSINIGPGRAFYTTGDIIGDIRQAHC	AF138100	1	true	false	false	false	false	false	false	false	false
CARPNNNTRKSINIGPGRAWYATGEIIGDIRKAHC	JN856490	0	true	false	false	false	true	false	false	false	false
CARPNNNTRKSIPIGPGRAFFATGDIIGNIRQAHC	AY653714	0	false	false	false	false	false	false	true	false	false
CARPNNNTRKSIPMGPGRAFYATGDIIGDVRQAHC	EU700564	2	true	false	false	false	false	false	false	false	false
CARPNNNTRKSIRIGPGQAFFATNGVIGDIRQAHC	KF039207	2	true	false	false	false	false	false	false	false	false
CARPNNNTRKSIRIGPGQTFYATGDIIGDIRKAHC	FJ541850	2	true	false	false	false	false	true	false	false	false
CARPNNNTRKSIRIGPGQTFYATGDIIGNIREAHC	DQ381972	0	true	false	false	false	false	false	false	false	false
CARPNNNTRKSIRIGPGQTFYATGDIVGDIRKAHC	KM513817	2	false	false	false	false	false	false	false	false	true
CARPNNNTRKSIRIGPGQTIYATGDIIGEIRQAHC	JX993338	0	true	false	true	false	false	false	false	false	false
CARPNNNTRKSITIGPGRAFYATGDIIGNIRQAHC	KM353812	2	false	false	true	false	false	false	false	false	false
CARPNNNTRKSMRIGPEQTFYATGDIIGDIRQAHC	KU611625	4	true	false	false	false	false	false	false	false	false
CARPNNNTRKSMRIGPGQTFFATGDIIGDIRQAHC	HM638983	1	true	false	false	false	false	true	false	false	false
CARPNNNTRKSMRIGPGQTFYATGEIIGNIRQAHC	KU865729	1	true	false	false	false	true	false	false	false	false
CARPNNNTRKSVRIGPGQTFYATGAVTGDTRQAHC	MT227436	4	false	false	false	false	false	true	false	false	false
CARPNNNTRKSVRIGPGQTFYATGDIIGDIRKAHC	FJ541819	0	true	false	false	false	false	true	false	false	false
CARPNNNTRKSVRIGPGQTFYATGDIIGDIRQAHC	KY112361	3	true	false	false	false	true	false	false	false	false
CARPNNNTRKSVRIGPGQTFYATKDIIGDIRQAHC	HM036742	1	true	false	false	true	false	false	false	false	false
CARPNNNTRKSVRIGPGQTIFATKDIIGDIRQAHC	HM036741	3	false	false	false	true	false	false	false	false	false
CARPNNNTRKTVGIGPGQTFYATGDIIGDIREAHC	GU201640	1	true	false	false	false	false	false	false	false	false
CARPNNNTRQGIHMGPGRSFYTAGAIIGDIRQAHC	EU700750	2	true	false	false	false	false	false	false	false	false
CARPNNNTRQSIRIGPGQTLYTTEIIGDIRQAHC	AY931518	3	false	false	false	true	false	false	false	false	false
CARPNNNTRQSVRIGPGQTFYATGDIIGDIRQAHC	KF374634	1	true	false	false	false	false	false	false	false	false
CARPNNNTRRSIHIGPGKAFYTGDIIGNIRQAHC	DQ143659	4	false	false	true	false	false	false	false	false	false
CARPNNNTRRSINIGPGRAFHTTGQIIGNIRQAHC	HM002319	0	false	false	false	false	false	false	true	false	false
CARPNNNTRRSINIGPGRAFYATGEIIGDIRQAHC	U16477	0	true	false	false	false	false	false	false	false	false
CARPNNNTRRSINIGPGRAWYAIGDIIGDIRKAHC	JN856507	4	true	false	false	false	true	false	false	false	false
CARPNNNTRRSIPIGPGRAFYATGEIIGDIRQAYC	JN856645	1	false	false	false	false	true	false	false	false	false
CARPNNNTRRSMNIGPGRAFHTTGQIIGNIRQAHC	HM002326	3	false	false	false	false	false	false	true	false	false
CARPNNNTRRSVRIGPGQAFYTTGEIIGDTRQAHC	KC187315	2	true	false	true	false	false	false	false	false	false
CARPNNNTRSSIHMGPGKAFYTTGDIIGDIRQAHC	JN786692	3	false	false	false	false	false	false	false	false	true

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Dataset Description

Dataset Summary

This dataset was derived from the Los Alamos National Laboratory HIV sequence (LANL) database. It contains 5,510 unique V3 sequences, each annotated with its corresponding bodysite that it was associated with. Supported Tasks and Leaderboards: None

Languages: English

Dataset Structure

Data Instances

Data Instances: Each column represents the protein amino acid sequence of the HIV V3 loop. The ID field indicates the Genbank reference ID for future cross-referencing. There are 2,935 total V3 sequences, with 91% being CCR5 tropic and 23% CXCR4 tropic. Data Fields: ID, sequence, fold, periphery-tcell, periphery-monocyte, CNS, lung, breast-milk, gastric, male-genitals, female-genitals, umbilical-cord, organ Data Splits: None

Dataset Creation

Curation Rationale:

Initial Data Collection and Normalization: Dataset was downloaded and curated on 12/20/2021.

Considerations for Using the Data

Social Impact of Dataset: This dataset can be used to study the mechanism by which HIV V3 loops allow for study of HIV compartmentalization.

Discussion of Biases: DDue to the sampling nature of this database, it is predominantly composed of subtype B sequences from North America and Europe with only minor contributions of Subtype C, A, and D. Currently, there was no effort made to balance the performance across these classes. As such, one should consider refinement with additional sequences to perform well on non-B sequences. Additionally, this dataset is highly biased to peripheral T-cells.

Additional Information:

Dataset Curators: Will Dampier
Citation Information: TBA

license: mit

Downloads last month: 111

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Size of downloaded dataset files:

116 kB

Size of the auto-converted Parquet files:

116 kB

Number of rows:

5,447

Models trained or fine-tuned on damlab/HIV_V3_bodysite

damlab/HIV_V3_bodysite

Text Classification • Updated Feb 24, 2022 • 8