SMILE 1.44 Structured Motif Inference and Evaluation, with 2 boxes L. Marsan, J. Allali Marsan L, Sagot MF (2001). Algorithms for extracting structured motifs using a suffix-tree with application to promoter and regulatory site consensus identification. J. of Computational Biology, 7:345-360. smile2 smile2 perl "smile params" 0 param params seq Sequences File perl "FASTA file\t\t\t$value\\n" 1 8 1 params alphabet Alphabet params perl "Alphabet file\t\t\t/local/gensoft/lib/SMILE/$value\\n" dna.alphabet 2 dna.alphabet dnadeg.alphabet aa-barton.alphabet aa-smiths.alphabet how_many_N perl $alphabet ne "dna.alphabet" 0 Maximum number of N in a motif (degenerated DNA or protein alphabet) perl "Composition in *\t\t$value\\n" 3 params how_many_R perl $alphabet eq "dnadeg.alphabet" 0 Maximum number of R (purine) in a motif (degenerated DNA) perl "Composition in AG\t\t$value\\n" 3 params how_many_Y perl $alphabet eq "dnadeg.alphabet" 0 Maximum number of Y (pyrimidine) in a motif (degenerated DNA) perl "Composition in CT\t\t$value\\n" 3 params quorum Minimum percentage of sequences containing a motif (quorum) (enter a value between 0 and 100) perl "Quorum\t\t\t\t$value\\n" (enter a value between 0 and 100) perl $value > 100 || $value < 0 params 10 minlen Total min length perl "Total min length\t\t$value\\n" params 11 Length parameters should be close to the expected motifs. A too large range between min/max might produce too many insignificant results. maxlen Total max length perl (defined $value)? "Total max length\t\t$value\\n" : "Total max length\t\t0\\n" params 12 Total length of concatened boxes. subst Total substitutions perl "Total substitutions\t\t$value\\n" params 13 Too many substitutions (number of substitutions must be smaller than min length) perl defined $subst && ! ($subst < $minlen) minspacer Min spacer length perl "Min spacer length\t\t$value\\n" params 150 This parameter describes the minimum distance between the 2 boxes. maxspacer Max spacer length perl "Max spacer length\t\t$value\\n" params 150 This parameter describes the maximum distance between the 2 boxes. boxes perl "Boxes\t\t\t\t2\\n" 1 params 70 shuffling perl "\\nShufflings\t\t\t\t100\\n" 1000 params kmer perl "Size k-mer\t\t\t\t2\\n" 1000 params result perl "Output file\t\t\tsmile.result\\n" 1 params box1_options Box 1 Parameters box1_label perl "\\nBOX 1 =========================\\n" 110 params minlen1 Min length of box 1 perl "Min length\t\t$value\\n" params 111 maxlen1 Max length of box 1 perl (defined $value)? "Max length\t\t$value\\n" : "Max length\t\t0\\n" params 112 subst1 Substitutions perl "Substitutions\t\t$value\\n" params 113 Too many substitutions (number of substitutions must be smaller than min length) perl defined $subst1 && ! ($subst1 < $minlen1) box2_options Box 2 Parameters box2_label perl "\\nBOX 2 =========================\\n" 210 params minlen2 Min length of box 2 perl "Min length\t\t$value\\n" params 211 maxlen2 Max length of box 2 perl (defined $value)? "Max length\t\t$value\\n" : "Max length\t\t0\\n" params 212 subst2 Substitutions perl "Substitutions\t\t$value\\n" params 213 Too many substitutions (number of substitutions must be smaller than min length) perl defined $subst2 && ! ($subst2 < $minlen2) resultsfiles smile.result smile.result.shuffle