Protein Construct Tools

Description

A small python library written to import cDNA sequences from NCBI database and form chimeric protein constructs.

Dependencies

• Biopython

Install

• Written for python 3

• Install requirements

  pip install -r requirements.txt

Use

1. Import Sequence Tools

   from SequenceTools import SequenceTools

2. Create a SequenceTools object with your email

   tools = SequenceTools(email="your@email.com")

   For NCBI api key:

   tools = SequenceTools(apiKey="api_key", email="your@email.com")

3. Import Sequence from NCBI UniGene

   tools.importSeqeuenceByNCBIIdentifier("AK079513.1")

4. Deconstruct imported sequence and give deconstruction key

   tools.deconstructImportedCDNASequence(tools.allSequences["AK079513.1"], "AK079513.1")

5. Make new deconstructed sequence from range to isolate portion (in this example the extracellular peptides) and give key.

   tools.makeNewDeconstructedSequenceFromDeconstructedSequencePeptideRange(tools.allDeconstructedSequences["AK079513.1"], 24, 244, "CD86_Extracellular")

6. Create sequences from copied DNA of other proteins, etc.

   nhe1Seq = tools.createSeqObjectFromString("GCTAGC")

7. Deconstruct sequences, give key for reference, and specify if coding

   tools.deconstructDNASequence(nhe1Seq, "NheI", False)

8. Make a new construct from deconstructed sequences and give a key

   tools.createConstructFromDeconstructedSequences(['NheI' ,'SecretionSignal', 'Linker1', 'CD86_Extracellular', "Linker2", 'APTag', 'Linker3', 'TEV', 'HIS','STOPS', 'EcoRI'], 'NheI-CD86Extracellular-APTag-TEV-HIS-EcoRI')

9. Compare construct with seq

   comp5 = tools.compareDNAConstructToSequence(tools.allConstructs['NheI-CD86Extracellular-APTag-TEV-HIS-EcoRI'], genScriptSeq)

Contact

For new feature requests or debugging contact: arosad2@protonmail.ch.