DeepMutSim 1.0.0

Generates all possible SNVs for MANE transcripts using HGVS nomenclature.

DeepMutSim

DeepMutSim generates simulations for all possible single nucleotide variants (SNVs) for the Matched Annotation from NCBI and EMBL-EBI (MANE) transcript, along with the corresponding protein using HGVS notation.

INSTALLATION

pip install deepmutsim

CONFIGURATION (Mandatory)

Before you can use DeepMutSim, you must set two environment variables to query the NCBI Entrez database.

EMAIL: (Required by NCBI) A valid email address so NCBI can contact you if there's an issue with your queries.

API_KEY: (Recommended) An NCBI API key, which allows for a much higher query rate. You can obtain one from your NCBI account settings.

Linux/macOS:

export EMAIL="[e-mail]"
export API_KEY="your_api_key_here"

Windows (PowerShell):

set EMAIL="[e-mail]"
set API_KEY="your_api_key_here"

USAGE

Variant Simulator

import deepmutsim
# Assumes EMAIL and API_KEY are set
deepmutsim.cds("INS")

[('NM_000207.3:c.1A>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.1A>T', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.1A>C', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.2T>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.2T>A', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.2T>C', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.3G>A', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.3G>T', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.3G>C', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ... ('NM_000207.3:c.328A>T', 'NP_000198.1:p.(N110Y)', 'NP_000198.1:p.(Asn110Tyr)'), ('NM_000207.3:c.328A>C', 'NP_000198.1:p.(N110H)', 'NP_000198.1:p.(Asn110His)'), ('NM_000207.3:c.329A>T', 'NP_000198.1:p.(N110I)', 'NP_000198.1:p.(Asn110Ile)'), ('NM_000207.3:c.329A>C', 'NP_000198.1:p.(N110T)', 'NP_000198.1:p.(Asn110Thr)'), ('NM_000207.3:c.330C>T', 'NP_000198.1:p.(N110=)', 'NP_000198.1:p.(Asn110=)'), ('NM_000207.3:c.330C>A', 'NP_000198.1:p.(N110=)', 'NP_000198.1:p.(Asn110=)'), ('NM_000207.3:c.330C>G', 'NP_000198.1:p.(N110=)', 'NP_000198.1:p.(Asn110=)')]

deepmutsim.utr5("INS")

['NM_000207.3:c.-59A>G', 'NM_000207.3:c.-59A>T', 'NM_000207.3:c.-59A>C', 'NM_000207.3:c.-58G>A', 'NM_000207.3:c.-58G>T', ... 'NM_000207.3:c.-2C>A', 'NM_000207.3:c.-2C>T', 'NM_000207.3:c.-1C>G', 'NM_000207.3:c.-1C>A', 'NM_000207.3:c.-1C>T']

deepmutsim.utr3("INS")

['NM_000207.3:c.*1A>G', 'NM_000207.3:c.*1A>T', 'NM_000207.3:c.*1A>C', 'NM_000207.3:c.*2C>G', 'NM_000207.3:c.*2C>A', ... 'NM_000207.3:c.*72G>T', 'NM_000207.3:c.*72G>C', 'NM_000207.3:c.*73C>G', 'NM_000207.3:c.*73C>A', 'NM_000207.3:c.*73C>T']

deepmutsim.splice_site("INS")

['NC_000011.10(NM_000207.3):c.187+1G>A', 'NC_000011.10(NM_000207.3):c.187+1G>T', 'NC_000011.10(NM_000207.3):c.187+1G>C', 'NC_000011.10(NM_000207.3):c.187+2T>A', 'NC_000011.10(NM_000207.3):c.187+2T>G', 'NC_000011.10(NM_000207.3):c.187+2T>C', 'NC_000011.10(NM_000207.3):c.188-2A>G', 'NC_000011.10(NM_000207.3):c.188-2A>T', 'NC_000011.10(NM_000207.3):c.188-2A>C', 'NC_000011.10(NM_000207.3):c.188-1G>A', 'NC_000011.10(NM_000207.3):c.188-1G>T', 'NC_000011.10(NM_000207.3):c.188-1G>C']