Crate imgt 

IMGT

Handle the IMGT database of antibody germlines easily.

Library features

• Access to all germlines from all species in IMGT
• Access to all isotopes of the germlines
• Access to the regions (CDRs etc) and annotations (conserved etc)
• Single threaded and multi threaded access

Example usage

use imgt::*;
let selection = Selection::default()
    .species([Species::HomoSapiens])
    .chain([ChainType::Heavy])
    .gene([GeneType::V]);
let first = selection.germlines(&STATIC_IMGT).next().unwrap();
assert_eq!(first.name(), "IGHV1-2*01");

Compilation features

• rayon - enables parallel iterators using rayon This crate handles parsing the IMGT LIGM-DB database into structures compatible with mzcore. It additionally stores all regions and annotations. There are two main ways of selecting germline(s), specified by name get_germline or by building a query over the data Selection.

Data present per species

Anarhichas minor / Spotted wolffish

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	2/0	2/0

Number of genes / number of alleles

Bos taurus / Domestic bovine

Kind	V	J	C
IGHV	12/13	10/16	8/18
IGKV	8/8	5/5	1/1
IGLV	30/31	8/8	4/4
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Camelus dromedarius / Arabian camel

Kind	V	J	C
IGHV	26/26	7/7	11/10
IGKV	10/10	5/5	1/1
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Canis lupus familiaris / Domestic dog

Kind	V	J	C
IGHV	37/37	6/6	8/7
IGKV	20/52	5/5	1/2
IGLV	86/86	9/9	9/9
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Capra hircus / Domestic goat

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	8/8	4/4	1/1
IGLV	24/24	2/2	1/1
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Carcharhinus plumbeus / Sandbar shark

Kind	V	J	C
IGHV	0/0	1/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Cercocebus atys / Sooty mangabey

Kind	V	J	C
IGHV	0/0	0/0	4/4
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Chaenocephalus aceratus / Blackfin icefish

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Cyprinus carpio / Common carp

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	22/0

Number of genes / number of alleles

Danio rerio / Zebrafish

Kind	V	J	C
IGHV	40/40	8/7	1/1
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	5/5	7/4	8/3

Number of genes / number of alleles

Dicentrarchus labrax / European seabass

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	22/0

Number of genes / number of alleles

Equus caballus / Domestic horse

Kind	V	J	C
IGHV	28/34	12/9	11/30
IGKV	19/23	4/5	1/2
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Felis catus / Domestic cat

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	13/13	5/5	1/1
IGLV	34/34	12/12	5/5
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Gadus morhua / Atlantic cod

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	3/3	1/0	2/0

Number of genes / number of alleles

Gallus gallus / Domestic chicken

Kind	V	J	C
IGHV	2/2	1/1	1/0
IGKV	0/0	0/0	0/0
IGLV	2/3	1/1	1/1
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Gasterosteus aculeatus / Three-spined stickleback

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	1/0

Number of genes / number of alleles

Ginglymostoma cirratum / Nurse shark

Kind	V	J	C
IGHV	0/0	8/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Gorilla gorilla / Western gorilla

Kind	V	J	C
IGHV	0/0	0/0	2/2
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Gorilla gorilla gorilla / Western lowland gorilla

Kind	V	J	C
IGHV	58/103	7/11	11/18
IGKV	29/53	5/6	1/1
IGLV	36/63	8/9	6/12
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Heterodontus francisci / Horn shark

Kind	V	J	C
IGHV	1/1	4/0	1/1
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Homo sapiens / Human

Kind	V	J	C
IGHV	81/320	9/18	12/94
IGKV	64/116	5/8	1/4
IGLV	51/113	7/10	7/15
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Hydrolagus colliei / Spotted ratfish

Kind	V	J	C
IGHV	0/0	1/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Hylobates lar / Common gibbon

Kind	V	J	C
IGHV	0/0	0/0	2/3
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Ictalurus punctatus / Channel catfish

Kind	V	J	C
IGHV	32/32	20/19	3/4
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	4/4	5/0	16/0

Number of genes / number of alleles

Lemur catta / Ring-tailed lemur

Kind	V	J	C
IGHV	58/58	7/7	3/3
IGKV	11/22	5/7	1/2
IGLV	133/133	10/10	8/8
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Leucoraja erinacea / Little skate

Kind	V	J	C
IGHV	1/1	3/2	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca arctoides / Stump-tailed macaque

Kind	V	J	C
IGHV	0/0	0/0	1/1
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca cyclopis / Taiwan macaque

Kind	V	J	C
IGHV	0/0	0/0	1/2
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca fascicularis / Crab-eating macaque

Kind	V	J	C
IGHV	67/67	7/7	7/12
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca mulatta / Rhesus monkey

Kind	V	J	C
IGHV	127/317	7/11	8/43
IGKV	91/136	5/5	1/2
IGLV	75/113	8/9	6/9
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca nemestrina / Pig-tailed macaque

Kind	V	J	C
IGHV	0/0	0/0	5/6
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca silenus / Liontail macaque

Kind	V	J	C
IGHV	0/0	0/0	1/1
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Macaca thibetana / Pere David’s macaque

Kind	V	J	C
IGHV	0/0	0/0	1/1
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mesocricetus auratus / Golden hamster

Kind	V	J	C
IGHV	0/0	0/0	7/7
IGKV	0/0	0/0	1/1
IGLV	0/0	0/0	3/3
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Monodelphis domestica / Gray short-tailed opossum

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus cookii / Cook’s mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	1/1
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus minutoides / Southern African pygmy mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	1/1
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus musculus / House mouse

Kind	V	J	C
IGHV	356/500	4/8	9/36
IGKV	120/141	5/10	1/1
IGLV	3/5	6/6	4/5
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus musculus castaneus / Southeastern Asian house mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	2/2	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus musculus domesticus / Western European house mouse

Kind	V	J	C
IGHV	2/1	4/1	2/1
IGKV	2/7	3/0	0/0
IGLV	0/0	2/2	2/2
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus musculus molossinus / Japanese wild mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	2/2	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus musculus musculus / Eastern European house mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	1/1	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus pahari / Shrew mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	1/1
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus saxicola / Spiny mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	1/1
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus sp. / Mice

Kind	V	J	C
IGHV	0/0	4/3	0/0
IGKV	1/1	4/0	1/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mus spretus / Western wild mouse

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	2/2	0/0	1/1
IGLV	2/2	2/2	2/3
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Mustela putorius furo / Domestic ferret

Kind	V	J	C
IGHV	43/43	7/7	5/5
IGKV	42/42	5/5	1/1
IGLV	46/46	8/8	7/5
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Neogale vison / American mink

Kind	V	J	C
IGHV	25/25	6/6	6/6
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Notothenia coriiceps / Black rockcod

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Oncorhynchus mykiss / Rainbow trout

Kind	V	J	C
IGHV	58/61	22/25	3/6
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	8/8	7/0	8/0

Number of genes / number of alleles

Ornithorhynchus anatinus / Platypus

Kind	V	J	C
IGHV	36/36	11/11	8/7
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Oryctolagus cuniculus / Rabbit

Kind	V	J	C
IGHV	33/33	6/11	17/24
IGKV	65/67	8/19	2/10
IGLV	22/22	4/4	6/7
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Oryctolagus cuniculus algirus / European rabbit

Kind	V	J	C
IGHV	0/0	0/0	1/3
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Oryctolagus cuniculus cuniculus / Rabbit

Kind	V	J	C
IGHV	0/0	0/0	1/5
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Ovis aries / Domestic sheep

Kind	V	J	C
IGHV	0/0	6/6	0/0
IGKV	6/6	4/4	1/1
IGLV	52/62	2/2	1/2
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Pan troglodytes / Chimpanzee

Kind	V	J	C
IGHV	0/0	0/0	3/3
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Papio anubis anubis / Olive baboon anubis

Kind	V	J	C
IGHV	0/0	0/0	4/4
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Pongo abelii / Sumatran orangutan

Kind	V	J	C
IGHV	70/135	7/13	11/31
IGKV	37/59	4/4	1/1
IGLV	33/56	7/9	5/11
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Pongo pygmaeus / Bornean orangutan

Kind	V	J	C
IGHV	70/99	7/9	13/17
IGKV	40/61	5/5	1/2
IGLV	37/55	7/9	5/8
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Protopterus aethiopicus / Marbled lungfish

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Raja eglanteria / Clearnose skate

Kind	V	J	C
IGHV	0/0	2/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Rattus norvegicus / Norway rat

Kind	V	J	C
IGHV	152/152	4/4	11/11
IGKV	39/39	7/7	1/2
IGLV	13/17	6/7	4/7
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Rattus rattus / Black rat

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Salmo salar / Atlantic salmon

Kind	V	J	C
IGHV	81/91	19/21	6/9
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	3/3	13/0	19/2

Number of genes / number of alleles

Salmo trutta / River trout

Kind	V	J	C
IGHV	0/0	0/0	2/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Seriola quinqueradiata / Japanese amberjack

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	22/0

Number of genes / number of alleles

Siniperca chuatsi / Mandarin fish

Kind	V	J	C
IGHV	0/0	0/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	5/0	5/0

Number of genes / number of alleles

Sus scrofa / Domestic pig

Kind	V	J	C
IGHV	5/5	5/6	12/20
IGKV	13/23	5/9	1/2
IGLV	12/17	3/4	2/2
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Trematomus bernacchii / Emerald rockcod

Kind	V	J	C
IGHV	0/0	0/0	1/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Vicugna pacos / Alpaca

Kind	V	J	C
IGHV	4/4	7/7	7/7
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Xenopus laevis/gilli / African or Cape clawed frog

Kind	V	J	C
IGHV	4/4	0/0	0/0
IGKV	0/0	0/0	0/0
IGLV	0/0	0/0	0/0
IGIV	0/0	0/0	0/0

Number of genes / number of alleles

Structs

Allele

A returned allele

AnnotatedSequence

Intermediate representation for annotated sequence

Chain

The intermediate representation for a chain

Gene

A germline gene name, broken up in its constituent parts.

Germline

Intermediate representation for germline

Germlines

A selection of germlines from a single species.

IMGT

IMGT antibody germlines

NotASpecies

Error type to indicate that the given name was not a recognised species from the IMGT database

Selection

The selection rules for iterating over a selection of germlines.

Enums

AlleleSelection

The allele handling strategy

ChainType

Any chain type of germline

Constant

Any type of constant gene

GeneType

Any gene in a germline, eg variable, joining

Species

All species available in the IMGT dataset. Look at the main documentation to see which actually have data provided.

Statics

STATIC_IMGT

A single shared static access to the static data in the ontologies for cases where no runtime resolution is needed (like tests).

Traits

FancyDisplay

Display things and allow the use of fancy non ascii characters