BOXSHADE 3.33 printouts from multiple-aligned protein or DNA sequences Hofmann, Baron alignment:multiple display boxshade boxshade perl "boxshade < params" 0 alignment Alignment File perl "$value\\n" 1 100 params readseq_ok_alig perl 1 input_format perl "2\\n" 2 params output_params Output parameters output_format Output format perl "$value\\n" e 3 1 2 3 4 6 7 8 9 a c d e params print_name Should sequence name be printed perl ($value)? "y\\n" : "n\\n" 1 13 params ruler Display ruler line perl ($value)? "y\\n" : "n\\n" 0 6 params space_between_name_sequence How many spaces between name and sequence perl "$value\\n" 1 15 perl $print_name params ignored_gaps Number of gaps to be ignored when shading (-1: none) perl (defined $value && $value != $vdef)? "$value\\n" : "\\n" 0 11 perl $output_format ne "b" params sequence_characters How many sequence characters per line perl "$value\\n" 60 12 params maximum is 254 perl $value > 254 lines How many lines between two sequence blocks perl "$value\\n" 1 17 params Enter a value > 0 perl defined $value && $value < 1 character_size Character size in Points (except for HTML and ASCII output formats) perl (defined $value && $value != $vdef)? "$value\\n" : "\\n" 10 28 perl $output_format ne "b" && $output_format ne "e" params save_shading Save Shading/Text perl "$value\\n" T 29 S T perl $output_format eq "d" params rotate Rotate plot perl ($value)? "y\\n" : "n\\n" 0 31 perl $output_format eq "1" || $output_format eq "3" || $output_format eq "d" params sequence_params Sequence properties label_similar Special label for similar residues perl ($value)? "y\\n" : "n\\n" 1 18 params label_identical Special label for identical residues in all sequences perl ($value)? "y\\n" : "n\\n" 0 19 params consensus Display consensus line perl ($value)? "y\\n .*\\n" : "n\\n" 0 5 params threshold Identity threshold perl (defined $value && $value != $vdef)? "$value\\n" : "\\n" 0.50 10 The threshold is the fraction of residues that must be identical or similar for shading to occur. The fraction must be between 0 and 1 perl defined $value && ($threshold <= 0 || $threshold > 1) perl $output_format ne "b" params letters Letters foreground and background colors different_background Background for different residues perl "$value\\n" W 20 B W 1 2 3 4 R G L Y M C perl $output_format ne "b" params different_foreground Foreground for different residues (lowercase choices mean lowercase letters in the sequence) perl "$value\\n" B 21 B b W w 1 2 3 4 5 6 7 8 R r G g L l Y y M m C c params identical_background Background for identical residues perl "$value\\n" B 22 B W 1 2 3 4 R G L Y M C perl $output_format ne "b" params identical_foreground Foreground for identical residues (lowercase choices mean lowercase letters in the sequence) perl "$value\\n" W 23 B b W w 1 2 3 4 5 6 7 8 R r G g L l Y y M m C c params similar_background Background for similar residues perl "$value\\n" 1 24 B W 1 2 3 4 R G L Y M C perl $label_similar && $output_format ne "b" params similar_foreground Foreground for similar residues (lowercase choices mean lowercase letters in the sequence) perl "$value\\n" B 25 B b W w 1 2 3 4 5 6 7 8 R r G g L l Y y M m C c perl $label_similar params conserved_background Background for conserved residues (if special label for identical residues) perl "$value\\n" 1 26 B W 1 2 3 4 R G L Y M C perl $label_identical && $output_format ne "b" params conserved_foreground Foreground for conserved residues (lowercase choices mean lowercase letters in the sequence) perl "$value\\n" B 27 B b W w 1 2 3 4 5 6 7 8 R r G g L l Y y M m C c perl $label_identical params single_comparison Comparison to a single sequence single Similarity to a single sequence perl ($value)? "y\\n" : "n\\n" 0 4 perl $output_format ne "b" params seq_no Which sequence (give its number) perl "$value\\n" 1 40 Give a sequence NUMBER perl ($value !~ /^\\d+$/) tcl [regexp {/^\\d+$/} $value match] Give a sequence NUMBER perl ($value !~ /^\\d+$/) tcl [regexp {/^\\d+$/} $value match] perl $single params hide Hide this sequence perl ($value)? "y\\n" : "n\\n" 0 41 perl $single params show_normal Show this sequence in all-normal rendition perl ($value)? "y\\n" : "n\\n" 0 42 perl $single params matrix Create identity / similarity matrix perl ($value)? "y\\n" : "n\\n" 0 34 params print_position perl "0\\n" 14 perl ! $ruler params outfile perl "boxshade.result\\n" "boxshade.result" 32 perl $output_format ne "1" && $output_format ne "e" && $output_format ne "2" && $output_format ne "d" params psfile perl "boxshade.ps\\n" "boxshade.ps" 33 perl $output_format eq "1" || $output_format eq "2" params htmlfile perl "boxshade.html\\n" "boxshade.html" 33 perl $output_format eq "e" params pictfile perl "boxshade.pict\\n" "boxshade.pict" 33 perl $output_format eq "d" params matrixfile perl "boxshade.matrix\\n" "boxshade.matrix" 35 perl $matrix params tmp_params params *.result *.pict