gnomic-grammar
v0.3.4
Published
A grammar for describing microbial genotypes and phenotypes.
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Gnomic
Gnomic is a grammar for describing genotypes and phenotypes of microbial strains. It is designed to provide an unambiguous, human and machine readable genotype definition notation with flexibility in the level of detail of the definition. The gnomic-grammar
NodeJS package contains methods for parsing and analysis of genotype definitions written in gnomic.
Installation
Install the gnomic-grammar
package via NPM:
npm install gnomic-grammar
Grammar
The grammar consists of a space- or *comma-*separated list of genotype or phenotype designations described using the following nomenclature:
Designation | Grammar expression
------------------------------------------- | -------------------------
feature
deleted | -feature
feature
inserted | +feature
site
replaced with feature
| site>feature
multiple integration site
replaced with feature
| site>>feature
feature
of organism
| organism/feature
feature
with mutation designation | feature(mutation-designation)
feature
with accession number | feature#GB:123456
feature
from accession number | #GB:123456
fusion of feature1
and feature2
| feature1:feature2
fusion
inserted at site
using marker
| site>fusion::marker+
phenotype: wild-type | phene+
or phene(wild-type)
phenotype: mutant | phene-
or phene
or phene(mutant)
selection marker: used (wild-type) | marker+
selection marker: available (missing/mutant) | marker-
a non-integrated plasmid | plasmid{}
or plasmid{feature, [...]}
plasmid with selection marker | plasmid{feature, [...]}::marker+
integrated vector/plasmid with mandatory integration site | site>vector{feature, [...]}
nucleotide range of a feature
| feature[startBase_endBase]
coding nucleotide range of a gene
| gene[c.startBase_endBase]
protein amino-acid range of a gene
| gene[p.startAA_endAA]
protein amino-acid of a gene
| gene[p.AA]
feature
of type promoter | promoter.promoterName
Term definitions
Term | Description
-------------- | --------------
gene
| a feature
that is a gene
feature
| a named DNA sequence such as a gene, promoter, or terminator
site
| a feature
(such as a gene
) with a specific location inside the genome of the original strain
phene
| an identifier for a feature
that comes with a variant definition.
marker
| a phenotype important for its role as a selection marker
Examples
| Example code | Description |
| ------------------------------------- | ------------------------------------- |
| X1>{abcD defG}::M2+, XII2>hijK::M2+, M3-
| integrate vector containg abcD
and defG
at X1
using M1
marker, insert hijK
at XII2
using M2
marker, state that M3
marker is available (mutant) in strain
| #SGD:YOR202W
| insertion of yeast gene 'YOR202W' referenced in the Saccharomyces Genome Database (SGD)|
| -CAB5#SGD:YDR196C
| deletion of yeast gene 'YDR196C' with standard name 'CAB5' referenced in SGD |
| +E.coli/abcD::Leu2+
| insertion of E.coli gene 'abcD' using 'Leu2' selection marker
| -abcD
| deletion of feature 'abcD' in the parent strain |
| +abcD::His5+
| insertion of feature 'abcD' using the 'His5' selection marker |
| efgH>abcD
| insertion of feature 'abcD' at the location of 'efgH', substituting (deleting) 'efgH' |
| abcD(cr)
| presence of gene 'abcD' with 'cr' (i.e. cold-resistant) mutation |
| +Pmtr:abcD:Trmt
| insertion of the fusion of features 'Pmtr', 'abcD', 'Trmt'
| +promoter.Pmtr:abcD:terminator.Trmt
| insertion of the fusion of features 'Pmtr', 'abcD', 'Trmt' with explicit types
| +abcD:efgH:His5+
| insertion of genes 'abcD' and 'efgH' next to each other using the 'His5' selection marker |
| Abc+
| Abc wild-type phenotype |
| Abc-
| Abc mutant phenotype |
| p123{}
| Plasmid p123
present |
| X1>p123{geneA geneB}::KanMX+
| Integration of p123
containing geneA
and geneB
at X1
using KanMX
marker |
Contributions
Contributions are very welcome. Please create an issue or contact the author (Lars Schöning) if you would like to propose any significant/breaking changes. Let us know if you want to help us out with a Python version of the grammar.