]> Calculates DNA RNA/DNA melting temperature (EMBOSS) nucleic:composition http://bioweb.pasteur.fr/docs/EMBOSS/dan.html dan &emboss_init; input Input section sequence sequence -- DNA [sequences] (-sequence) perl " -sequence=$value -sformat=fasta" 1 dna 8 seqsfile perl 1 required Required section windowsize Enter window size (-windowsize) 20 perl " -windowsize=$value" 2 The values of melting point and other thermodynamic properties of the sequence are determined by taking a short length of sequence known as a window and determining the properties of the sequence in that window. The window is incrementally moved along the sequence with the properties being calculated at each new position. 1 100 shiftincrement Enter Shift Increment (-shiftincrement) 1 perl " -shiftincrement=$value" 3 This is the amount by which the window is moved at each increment in order to find the melting point and other properties along the sequence. 1 acd $windowSize dnaconc Enter DNA concentration (nM) (-dnaconc) 50. perl " -dnaconc=$value" 4 1. 100000. saltconc Enter salt concentration (mM) (-saltconc) 50. perl " -saltconc=$value" 5 1. 1000. advanced Advanced section rna Use RNA data values (-rna) perl ($value)? " -rna" : "" 6 This specifies that the sequence is an RNA sequnce and not a DNA sequence. productsection Product options product Prompt for product values (-product) perl ($value)? " -product" : "" 7 This prompts for percent formamide, percent of mismatches allowed and product length. formamide Enter percentage of formamide (-formamide) perl $product acd $product 0. perl (defined $value && $value != $vdef)? " -formamide=$value" : "" 8 This specifies the percent formamide to be used in calculations (it is ignored unless -product is used). 0. 100. mismatch Enter percent mismatch (-mismatch) perl $product acd $product 0. perl (defined $value && $value != $vdef)? " -mismatch=$value" : "" 9 This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used). 0. 100. prodlen Enter the product length (-prodlen) perl $product acd $product acd $windowSize perl (defined $value && $value != $vdef)? " -prodlen=$value" : "" 10 This specifies the product length to be used in calculations (it is ignored unless -product is used). acd $windowSize thermosection Thermodynamic options thermo Thermodynamic calculations (-thermo) perl ($value)? " -thermo" : "" 11 Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file. temperature Enter temperature (-temperature) 25. perl (defined $value && $value != $vdef)? " -temperature=$value" : "" 12 If -thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values. 0. 100. output Output section plot Produce a plot (-plot) perl ($value)? " -plot" : "" 13 If this is not specified then the file of output data is produced, else a plot of the melting point along the sequence is produced. mintemp Enter minimum temperature (-mintemp) perl $plot acd $plot 55. perl (defined $value && $value != $vdef)? " -mintemp=$value" : "" 14 Enter a minimum value for the temperature scale (y-axis) of the plot. 0. 150. graph graph (-graph) x11 x11 hp7470 hp7470 postscript postscript cps cps hp7580 hp7580 null null data data colourps colourps text text none none tek4107t tek4107t tekt tekt xwindows xwindows hpgl hpgl xterm xterm meta meta ps ps tek tek png png tektronics tektronics perl $plot acd $plot postscript perl ($value)? " -graph=$value" : "" 15 outfile outfile (-outfile) acd @(!$(plot)) perl ($value)? " -outfile=$value" : "" 16 If a plot is not being produced then data on the melting point etc. in each window along the sequence is output to the file. auto perl " -auto -stdout" 18 psresults_graph perl $graph eq "postscript" || $graph eq "ps" || $graph eq "colourps" || $graph eq "cps" *.ps metaresults_graph perl $graph eq "meta" *.meta dataresults_graph perl $graph eq "data" *.dat pngresults_graph perl $graph eq "png" *.png *.2 *.3 hpglresults_graph perl $graph =~ /hp/ *.hpgl