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'FScanR' scans the target peptide sequences within the prodatency of the target cDNA or mRNA sequence and identifies PRF events according to BLASTX homolog sequence alignment to the library peptide sequences. The output format should be five columns or a tabular format as described in the previous section.
'FScanR' determines the five most favorable Qframe values (Qframe1 to Qframe5) that uses the 'CUScan' (statistic algorithm) in a hop-by-hop system to identify the most-likely frameshift site for each peptide length detected. The five Qframe values are 'NoCDS' (does not match to any coding region), 'Start', 'PartialCDS' (mapped to the start codon), 'StopStart' (mapped to the stop codon, start codon), 'Stop' (mapped to the stop codon), and 'InRun' (mapped to an intron region). From the five Qframed values, the Qframe2 is the most prone to frameshift site, followed by Qframe3, then Qframe1, then Qframe4. The 'PartialCDS' and 'StopStart' Qframes are data not significant for any finding of frameshift site. 'CUScan' is a Monte-Carlo simulation technique, in which all predicted frame shifts at each codon is calculated from the mismatch distances between the Y frame and
Cuscan software is available at: http://gladstone.temple.edu/penn/ Figure I: Qframe calculation. Start line is the top line with the highest score, followed by lines of decreasing score. The score is the sum of the mismatch distances of all mismatches at each position, divided by the residue size.* Frame1 is predicted at the residue at which the score reaches the highest point The following parameters should be set in 'FScanR' for the above-mentioned BLASTX and diamond BLASTX outputs: d2c66b5586