software for exon trapping Thomas and Skolnick A probabilistic model for detecting coding regions in DNA sequences. Alun Thomas and Mark H Skolnick, IMA Journal of Mathematics Applied in Medicine and Biology, 1994, 11, 149-160. nucleic:translation gene finding xpound xpound perl "xpound" 0 seq DNA sequence File perl " < $value" 2 Everything after a % on a line in the input file is ignored. Other than comment xpound expects only white space, which is also ignored, or IUPAC charaters: A C M G R S V T W Y H K D B N in upper or lower case. Characters which do not uniquely determine a base, such as N, B, S and so on, are all interpreted as a C. Xpound will not accept the IUPAC character -, all occurences of which should be stripped from the input file beforehand. 13 outfile perl " > xpound.out " xpound.out 10 report_options Report options report Reports regions of bases for which the probability of coding is high (xreport) perl ($value)? " ; xreport < xpound.out " : "" 1 20 cut_off Cut off value for report perl (defined $value and $value != $vdef )? " $value " : "" 0.75 21 perl $report min_length Minimum length value for report perl ($value and $value != $vdef )? " $value " : "" 0 22 perl $report report_file Report file perl ($value)? " > $value " : " > xreport.out " xreport.out 25 perl $report postscript_options Postscript options postscript Produces a file of graphs in PostScript format (xpscript) perl ($value)? "; xpscript " : "" 1 30 orientation Orientation perl ($value eq "lanscape")? " -l " : "" portrait 31 portrait portrait lanscape lanscape perl $postscript rows Rows of plots per page (-r) perl ($value and $value != $vdef )? " -r $value " : "" 5 32 perl $postscript columns Columns of plots per page (-c) perl ($value and $value != $vdef )? " -c $value " : "" 1 32 perl $postscript high Draw a line at this level (-hi) perl ($value and $value != $vdef )? " -hi $value " : "" 0.75 33 perl $postscript low Draw a line at this level (-hi) perl ($value and $value != $vdef )? " -lo $value " : "" 0.5 34 perl $postscript psfile PostScript file perl ($value)? " > $value" : " > xpound.ps" xpound.ps 100 perl $postscript result perl " xpound.out " 40 perl $postscript