PRSS/PRFX
PRSS/PRFX Evaluates the significance of pairwise similarity scores using a Monte Carlo analysis. The Smith-Waterman local similarity score for the two sequences is calculated, and then the statistical parameters Lambda and K from the random scores calculated by aligning the first sequence to 200 to 1000 times shuffles of the second sequence. PRFX does a similar shuffle, but compares a translated DNA sequence to a protein sequence using the FASTX algorithm.
PRSS/PRFX can either shuffle the second sequence in its entirety (uniform shuffling) or shuffle the second sequence in 20 residue segments (window shuffle). This latter strategy preserves local amino acid composition biases, e.g. in transmembrane segments. Part of the Fasta family.
Manual: http://www.med.nyu.edu/rcr/rcr/fastaman.html
INPUT = Nucleic Acid or Protein sequence files in fasta format. The search set is a single sequence.
TEST INPUT FILES
Input file: prssn1_in.txt
Input file: prssn2_in.txt
TEST OUTPUT FILES
Output file: prss_out1.txt