HERVd

What is ERV?

Analysis of the human genome revealed that some 45% of it consists of various kinds of transposable elements. Around 8% of the human DNA is derived from retrovirus-like elements. They originate from ancient retroviral infections or are relics of retroviral transposomal activity in the germ-line cells. Human endogenous retroviruses (HERVs) comprise a part of these elements. They have undergone substantial changes such as mutations of all kinds, deletions and insertions of other transposons, recombinations and mini- and micro-satellite expansion. This is why it is often difficult to identify individual retroviral genes and other retroviral DNA regions.

HERVs are classified according to several criteria that are, however, mostly artificial, especially in view of rearrangements and mutations changing the original retroviral DNA sequences.

HERVs became extremely useful tools in studying evolution and the plasticity of primate genomes. Some of them acquired important functions. For example, HERV long terminal repeats (LTRs) serve as transcription regulators, alternative promoters and polyadenylation signals for several cellular genes. Another function proposed for HERVs is in determining resistance to viral infections. The best example proposed for the HERV function is that the product of the HERV-W envelope gene on chromosome 7 is the human syncytin, which is a protein involved in the placenta formation. HERVs are likely to be cofactors in several diseases, such as multiple sclerosis, schizophrenia and cancer.

It is important to analyze the structure and distribution of HERVs and compare them with situations in other genomes, e.g. those of primates and the mouse. These comparisons may help to find genomic elements that contribute to developmental phenotypical differences between humans and other organisms. Precise localization and characterization of insertion sites may be useful for designing retroviral vectors for gene therapy.

API

Repeats, Elements and Entities are accesible via API with JSON format. API end-point: https://herv.img.cas.cz/api

Elements	/api/elements
Repeats	/api/repeats
Entities	/api/entities

Swagger definition	https://herv.img.cas.cz/api/swagger
Apiary	https://ervd.docs.apiary.io

Get elements

limit

Type:	Integer
Default:	25
Values:	1..100

name

Type:	String

type

Type:	String
Values:	DNA, ERV, LINE, Low_complexity, RC, Retroposon, RNA, Satellite, Simple_repeat, SINE, Unknown


GET https://herv.img.cas.cz/api/elements


curl --include \
     --header "Accept: application/json" \
     "https://herv.img.cas.cz/api/elements"

Get repeats

limit

Type:	Integer
Default:	25
Values:	1..100

name

Type:	String

type

Type:	String
Values:	DNA, ERV, LINE, Low_complexity, RC, Retroposon, RNA, Satellite, Simple_repeat, SINE, Unknown

sequence

Type:	String
Values:	chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY

sequence_begin

Type:	Integer
Values:	0..4294967295

sequence_end

Type:	Integer
Values:	0..4294967295


GET https://herv.img.cas.cz/api/repeats


curl --include \
     --header "Accept: application/json" \
     "https://herv.img.cas.cz/api/repeats"

Get entities

limit

Type:	Integer
Default:	25
Values:	1..100

name

Type:	String

type

Type:	String
Values:	DNA, ERV, LINE, Low_complexity, RC, Retroposon, RNA, Satellite, Simple_repeat, SINE, Unknown

subtype

Type:	String
Values:	INT, LTR

by_element

Type:	String

sequence

Type:	String
Values:	chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY

sequence_begin

Type:	Integer
Values:	0..4294967295

sequence_end

Type:	Integer
Values:	0..4294967295


GET https://herv.img.cas.cz/api/entities


curl --include \
     --header "Accept: application/json" \
     "https://herv.img.cas.cz/api/entities"

Swagger compatible API description


GET https://herv.img.cas.cz/api/swagger


curl --include \
     --header "Accept: application/json" \
     "https://herv.img.cas.cz/api/swagger"

Swagger compatible API description for specific API

name

Type:	String

locale

Type:	Symbol


GET https://herv.img.cas.cz/api/swagger/:name


curl --include \
     --header "Accept: application/json" \
     "https://herv.img.cas.cz/api/swagger/:name"

Database description

Elements

Concrete original element such as MLT1K, THE1B or AluSx. Accessible on Elements.

Name	Name of the element (MLT1K)
Type	SINE, LINE, ERV, DNA, ...
Subtype	Used only by ERV which have format: LTR-gag-pol(-env)-LTR . Subtype can br: LTR ... sequence on the edge INT ... collection of gag-pol-env
Size	Number of bases

Repeats

Part or full element found on genome. Values are almost the same as in RepeatMasker output. Accesible on Repeats.

Name	The same name as element
SW	Smith-Waterman score calculated by RepeatMasker
Div percent	% substitutions in matching region compared to the consensus
Del percent	% of bases opposite a gap in the query sequence (deleted bp)
Ins percent	% of bases opposite a gap in the repeat consensus (inserted bp)
Type	The same type as element.
Subtype	The same as element. See Elements section for more details.
Sequence	Name of the chromosome.
Notes	Notes or erros found during parsing RepeatMasker output. For example length is not match with element.
Sequence position	SEQUENCE: S_BEGIN - S_END (ORIENTATION)
Repeat position	R_BEGIN - R_END (left: R_LEFT)
Entity position	E_BEGIN - E_END (left: E_LEFT)

Entities

Entity is "thing" which is made by combination of element's repeats. For ERV type its represet the original retro-virus. More details are in section creating entities. Accessible on Entities.

Name	Format: ELEMENTS-TYPE__ID
Average SW	Total SW average of all repeats
Consensus size	How much of original entity is present on genome (how much remained).
Type	Type of elements
Subtype	Only on ERV. It represet what parts of entity remains. LIL = LTR-gag-pol-env-LTR

Creating entities

1. Data

This section describe how entities are created. The process is very simplified.

2. Creating raw entities

First all element's pieces are joined to create a "raw entity". That will look like this:

3. Create entities

Now LTR and INT are joined based on neighbors frequency.

4. Result

Now result will look like this

References

Endogenous retrovirus in Wikipedia from https://en.wikipedia.org/wiki/Endogenous_retrovirus
Pačes, J., Pavlíček, A., & Pačes, V. (2002). HERVd: database of human endogenous retroviruses. Nucleic Acids Research, 30(1), 205–206. Full text
RepeatMasker Documentation from http://www.repeatmasker.org/webrepeatmaskerhelp.html