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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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