oligoMass 0.0.3

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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

Getting started

####1) Calculate average and monoisotopic molecular weight of any deoxyoligonucleotides sequenses 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) 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

####4)Calc extinction coef: from oligoMass import dna

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

print(extinction)

# 55100