oligoMass 0.2.0

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Description

Calculation of oligonucleotides weights and some properties.

Installation

from Repository on GitHub:

pip install git+https://github.com/a1exsan/oligoMass.git#egg=oligoMass

from PyPi:

pip install oligoMass -U https://pypi.org/project/oligoMass/

Getting started

#### 1) Calculate average and monoisotopic molecular weight of any deoxyoligonucleotide sequense consists of #### five type bases: dA, dT, dG, dC, dU

from oligoMass.molmassOligo import oligoNASequence

oligos = oligoNASequence(‘ATGCCGGTuugtU’)

print(f”molecular formula: {oligos.getMolecularFormula()}”)

print(f”MW: {oligoNASequence(‘ATGCC’).getAvgMass()}”)

print(f”monoMW: {oligoNASequence(‘ATGCC’).getMonoMass()}”)

#### 2) Calculate average and monoisotopic molecular weight of some deoxyoligonucleotide modifications #### such as: LNA(+), ribo(r), 2’-O-Me (m) or Phosphorothioated DNA bases as entered (*)

print(f” MW: {oligoNASequence(‘+ATrG+CCmG*GTuu+gtU’).getMonoMass()}”)

#### 3) Universal sintax to add modifications:

print(f” MW: {oligoNASequence(‘ATGC’).getMonoMass()} Da”) #1173.82 Da

print(f” MW: {oligoNASequence(‘ATGC’).getMolecularFormula()} Da”) # C39H50N15O22P3

print(f” MW: {oligoNASequence(‘AT{CH2}GC’).getMonoMass()} Da”) #1187.85 Da

print(f” MW: {oligoNASequence(‘AT{CH2}GC’).getMolecularFormula()} Da”) # C40H52N15O22P3

print(f” MW: {oligoNASequence(‘AT{S|O}GC’).getMolecularFormula()} Da”) # C39H50N15O21P3S

that equal (‘AT{S|O}GC’ == ‘ATG*C’)

print(f” MW: {oligoNASequence(‘AT[CH2]GC’).getMonoMass()} Da”) #1187.85 Da

print(f” MW: {oligoNASequence(‘AT/CH2/GC’).getMonoMass()} Da”) #1187.85 Da

#### 4) getPrefix(index) and getSuffix(index) methods can return prefix and suffix of the sequence

print(oligoNASequence(‘+ATrG+CCmG*GTuu+gtU’).getPrefix(index=2)())

# +AT

print(oligoNASequence(‘+ATrG+CCmG*GTuu+gtU’).getSuffix(index=4)())

# CmG*GTuu+gtU

#### 5)Calc extinction coef:

from oligoMass import dna

extinction = dna.get_simple_ssdna_extinction(“ATGCTT”, dna.get_extinction_dict())

print(extinction)

# 55100