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This version of Iterative Alignment excludes the calculation of the optimal alignment between sequences and scores them only based on the composition per position in the peptide sequence.

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Sarikaya-Lab-GEMSEC/Iterative-Alignment-Gapless

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Reqs:

1) Each matrix you want to work with in a single run must be in the same folder as a ".csv" file. In the given format (see example matrix)

2) Each peptide dataset must be divided into high binders and low binders (or non-binders) and labled as "high.csv" and "low.csv" respectivly.
	a. Similar to the matrices each database that is needed to run in a single run, must be in a folder with each subfolder containg 
	   both the high and low files.
3) It is recomended to create a seperate folder for each result to save to, but not neccesary.

4) The iterations, cutoff, Dataset Selection, and Gap Penalty all must be positive integers. The perturb percentage must be 0 < x < 1.

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This version of Iterative Alignment excludes the calculation of the optimal alignment between sequences and scores them only based on the composition per position in the peptide sequence.

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