Fig. 2

Output example. An example of the fLPS output in (a) short and (b) long formats, with a graphic of the LPSs in (c) (this is not part of the actual output of the program). The output is for protein CRPAK_HUMAN, human cysteine-rich PAK1 inhibitor. a The short format is: sequence name; type of bias (SINGLE-residue, MULTIPLE-residue or WHOLE-sequence); ordinal number of the LPS for the sequence (they are sorted in increasing order of binomial P-value); start residue in sequence; end residue in sequence; total number of bias residues in the LPS; binomial P-value for the LPS; CB signature (the single-letter amino-acid code of the residues is listed in order of precedence within curly brackets). b Two examples of the extra fields in long output, corresponding to the short output in (a). The long format has the additional fields: sum of log(P) (the sum of the log P-values of each of the constituent biases in the LPS, prior to merging); start residue of a core subsequence with the highest density of bias residues; end residue of the core subsequence; the core subsequence; up to 10 residues of N-terminal sequence context for the LPS; the LPS subsequence; up to 10 residues of C-terminal sequence context. Each LPS is listed on one line, except that in long format there is an optional summary footer that can be output using the ‘–d’ option. This begins with the ‘<’ symbol and contains these fields: sequence name; sequence length; number of SINGLE-residue LPSs; number of MULTIPLE-residue LPSs; number of WHOLE-sequence biases. For the long format in (b), for brevity most of the duplicated fields are omitted from the short format shown in (a). c A graphic of the LPSs. Bias type information, etc. as in (a)