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'FScanR' identifies Programmed Ribosomal Frameshifting (PRF) events from BLASTX homolog sequence alignment between targeted genomic/cDNA/mRNA sequences against the peptide library of the same species or a close relative. The output by BLASTX or diamond BLASTX will be used as input of 'FScanR' and should be in a tabular format with 14 columns. As input to 'QStart' the BLASTX output should be present, also containing the best hit information (from BLASTX, if possible). There will be information on forward start codon (FSC), start codon (SC), and stop codon (SCT) of target sequence, forward and reverse hit sequences - this is the information used by 'FScanR' to detect ribosomal frameshifting events.
The alignment of all sequences classified as frameshift candidates will be clustered (at 30% identity and 40%), and consensus sequence will be generated via star alignment (using the alignment of the best hit, if possible). The consensus sequence will contain the following information: Start codon, stop codon, sequence length (in base pairs) and the number of start codon for the reverse hit. The consensus sequences will be similar to the reverse hit (if possible). The consensus sequence will be displayed with 2 double lines, between the first start codon and the forward hit, and between the stop codon and the reverse hit. Both gaps on the unaligned parts of the consensus sequences will be highlighted with stars on the consensus sequence. This consensus sequence is generated from 'QStart' and 'FStart'-processed data.
The average coverage of an amino acid residue is the number of peptide hits identified at each residue divided by the length of the peptide. It is a fraction ranging from 0 (unidentified peptides) to 1 (peptides perfectly mapped to the coding frame). When zooming in by residue it gives information on the average fraction of amino acid residues identified in a coding frame (noted with the average coverage with respect to the reference sequence). d2c66b5586