Feature Extraction Package for Biological Sequences Based on Mathematical Descriptors

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Xmer k-Spaced Ymer Composition Frequency (kGap).

To use this model, follow the example below:

To run the code (Example): $ python3.7 methods/Kgap.py -i input -o output -l label -k kgap -bef before -aft after -seq type


Where:

-i = Input - Fasta format file, E.g., test.fasta

-o = Output - CSV format file, E.g., test.csv.

-l = label - lncRNA, circRNA...

-k = gap - e.g., Frequency of kgap, E.g. 1 = A_A, 2 = A__A, 3 = A___A...

-bef = before - e.g., 1 = A_A, 2 = AA_A, 3 = AAA_A...

-aft = after - e.g., 1 = A_A, 2 = A_AA, 3 = A_AAA...

-seq = type of sequence, e.g., 1 = DNA, 2 = RNA and 3 = Protein

Running:

$ python3.7 methods/Kgap.py -i sequences.fasta -o sequences.csv -l test -k 1 -bef 1 -aft 2 -seq 1

Note Input sequences for feature extraction must be in fasta format.

Note This example will generate a csv file with the extracted features.