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Sequence assembler for amino acid subsequences. Takes a line-separated text file and returns the assembled/merged peptides (using Needleman-Wunsch global alignment) as a text file.

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griffincalme/AminoAcidSequenceAssembly

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AminoAcidSequenceAssembly

Sequence assembler for amino acid subsequences. Takes a line-separated text file and returns the assembled/merged peptides (using Needleman-Wunsch global alignment) as a text file.

RunProteinSequenceAssembly.py

Edit the RunProteinSequenceAssembly.py with your line-separated text file of peptide subsequences and run it.

ProteinSequenceAssemblyLib.py

Contains functions for the "RunProteinSequenceAssembly.py" script.


Validation Folder

ProteinSequenceAssembly_NW_Validation.py

Validates the algorithm by generating random polypeptides, randomly fragmenting them (in silico fragmentation), and running the assembly on the resulting subsequences. Probably needs more improvement.

FragmentationSimulator.py

Generates a random polypeptide and then fragments in silico at random combinations of sites. Outputs the simulated fragments in a txt file.

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Sequence assembler for amino acid subsequences. Takes a line-separated text file and returns the assembled/merged peptides (using Needleman-Wunsch global alignment) as a text file.

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