Module rustyms::imgt

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Only available with feature imgt. This crate handles parsing the IMGT LIGM-DB database into structures compatible with rustyms. 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

§Bos taurus / Domestic bovine

KindVJC
IGHV12/133/47/9
IGKV6/61/11/1
IGLV25/265/54/4
IGIV0/00/00/0

Number of genes / number of alleles

§Camelus dromedarius / Arabian camel

KindVJC
IGHV0/00/00/0
IGKV8/84/41/1
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Canis lupus familiaris / Domestic dog

KindVJC
IGHV35/355/54/6
IGKV19/394/41/2
IGLV71/719/99/9
IGIV0/00/00/0

Number of genes / number of alleles

§Capra hircus / Domestic goat

KindVJC
IGHV0/00/00/0
IGKV5/51/11/1
IGLV24/241/11/1
IGIV0/00/00/0

Number of genes / number of alleles

§Danio rerio / Zebrafish

KindVJC
IGHV35/357/71/1
IGKV0/00/00/0
IGLV0/00/00/0
IGIV3/33/33/3

Number of genes / number of alleles

§Equus caballus / Domestic horse

KindVJC
IGHV19/256/610/17
IGKV17/204/51/2
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Felis catus / Domestic cat

KindVJC
IGHV0/00/00/0
IGKV12/125/51/1
IGLV32/3210/105/5
IGIV0/00/00/0

Number of genes / number of alleles

§Gallus gallus / Domestic chicken

KindVJC
IGHV2/21/10/0
IGKV0/00/00/0
IGLV2/31/11/1
IGIV0/00/00/0

Number of genes / number of alleles

§Gorilla gorilla / Western gorilla

KindVJC
IGHV0/00/01/1
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Gorilla gorilla gorilla / Western lowland gorilla

KindVJC
IGHV53/955/811/18
IGKV26/505/61/1
IGLV27/436/66/12
IGIV0/00/00/0

Number of genes / number of alleles

§Homo sapiens / Human

KindVJC
IGHV56/1776/911/47
IGKV40/615/61/4
IGLV33/745/65/8
IGIV0/00/00/0

Number of genes / number of alleles

§Ictalurus punctatus / Channel catfish

KindVJC
IGHV23/2319/192/2
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Lemur catta / Ring-tailed lemur

KindVJC
IGHV56/564/43/3
IGKV11/224/51/2
IGLV119/11910/108/8
IGIV0/00/00/0

Number of genes / number of alleles

§Macaca fascicularis / Crab-eating macaque

KindVJC
IGHV1/16/61/1
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Macaca mulatta / Rhesus monkey

KindVJC
IGHV122/2797/118/16
IGKV59/785/51/2
IGLV55/747/76/9
IGIV0/00/00/0

Number of genes / number of alleles

§Mus cookii / Cook’s mouse

KindVJC
IGHV0/00/00/0
IGKV0/00/01/1
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Mus minutoides / Southern African pygmy mouse

KindVJC
IGHV0/00/00/0
IGKV0/00/01/1
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Mus musculus / House mouse

KindVJC
IGHV279/3924/69/22
IGKV102/1164/41/1
IGLV3/53/34/4
IGIV0/00/00/0

Number of genes / number of alleles

§Mus musculus domesticus / Western European house mouse

KindVJC
IGHV1/10/00/0
IGKV0/00/00/0
IGLV0/01/12/2
IGIV0/00/00/0

Number of genes / number of alleles

§Mus pahari / Shrew mouse

KindVJC
IGHV0/00/00/0
IGKV0/00/01/1
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Mus saxicola / Spiny mouse

KindVJC
IGHV0/00/00/0
IGKV0/00/01/1
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Mus spretus / Western wild mouse

KindVJC
IGHV0/00/00/0
IGKV0/00/01/1
IGLV2/20/01/2
IGIV0/00/00/0

Number of genes / number of alleles

§Mustela putorius furo / Domestic ferret

KindVJC
IGHV24/245/55/5
IGKV38/384/41/1
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Oncorhynchus mykiss / Rainbow trout

KindVJC
IGHV42/4519/233/5
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Ornithorhynchus anatinus / Platypus

KindVJC
IGHV34/3410/107/7
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Oryctolagus cuniculus / Rabbit

KindVJC
IGHV14/146/117/8
IGKV5/75/82/10
IGLV20/202/23/3
IGIV0/00/00/0

Number of genes / number of alleles

§Ovis aries / Domestic sheep

KindVJC
IGHV0/02/20/0
IGKV5/51/11/1
IGLV50/601/11/2
IGIV0/00/00/0

Number of genes / number of alleles

§Pongo abelii / Sumatran orangutan

KindVJC
IGHV47/473/37/7
IGKV30/304/41/1
IGLV25/254/45/5
IGIV0/00/00/0

Number of genes / number of alleles

§Pongo pygmaeus / Bornean orangutan

KindVJC
IGHV54/543/39/9
IGKV33/334/41/1
IGLV28/285/55/5
IGIV0/00/00/0

Number of genes / number of alleles

§Rattus norvegicus / Norway rat

KindVJC
IGHV122/1224/48/10
IGKV38/386/61/2
IGLV8/82/24/4
IGIV0/00/00/0

Number of genes / number of alleles

§Salmo salar / Atlantic salmon

KindVJC
IGHV69/7619/196/9
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

§Sus scrofa / Domestic pig

KindVJC
IGHV5/55/510/13
IGKV11/195/81/2
IGLV10/143/42/2
IGIV0/00/00/0

Number of genes / number of alleles

§Vicugna pacos / Alpaca

KindVJC
IGHV4/46/67/7
IGKV0/00/00/0
IGLV0/00/00/0
IGIV0/00/00/0

Number of genes / number of alleles

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

Structs§

  • Allele
    A returned allele
  • Gene
    A germline gene name, broken up in its constituent parts.
  • Selection
    The selection rules for iterating over a selection of germlines.

Enums§

  • AlleleSelection
    The allele handling strategy
  • Annotation
    Any annotation in a germline, eg conserved residues
  • ChainType
    Any chain type of germline
  • Constant
    Any type of constant gene
  • GeneType
    Any gene in a germline, eg variable, joining
  • Region
    Any region in a germline, eg FR1, CDR1
  • Species
    All species available in the IMGT dataset. Look at the main documentation to see which actually have data provided.

Traits§

  • FancyDisplay
    Display things and allow the use of fancy non ascii characters

Functions§