]> Generates a sparse protein signature (EMBOSS) protein:3d structure http://bioweb.pasteur.fr/docs/EMBOSS/siggen.html siggen &emboss_init; input input Section algpath Location of alignment files for input (-algpath) perl " -algpath=$value" 1 algextn Extension of alignment files for input (-algextn) .align perl " -algextn=$value" 2 required required Section sparsity % sparsity of signature (-sparsity) 10 perl " -sparsity=$value" 3 randomise Generate a randomised signature (-randomise) 0 perl ($value)? " -randomise" : "" 4 advanced advanced Section seqoption Select number -- Sequence variability scoring method [select values] (-seqoption) 1 Substitution matrix 2 Residue class 3 None , acd @(!$(randomise)) 3 perl " -seqoption=$value" 5 datafile Substitution matrix to be used (-datafile) 1 2 3 acd @($(seqoption)==1) ./EBLOSUM62 perl ($value && $value ne $vdef)? " -datafile=$value" : "" 6 conoption Select number -- Residue contacts scoring method [select values] (-conoption) 1 Number 2 Conservation 3 Number and conservation 4 None , acd @(!$(randomise)) 4 perl " -conoption=$value" 7 filtercon Ignore alignment positions making less than a threshold number of contacts (-filtercon) acd @(!$(randomise)) 0 perl ($value)? " -filtercon" : "" 8 conthresh Threshold contact number (-conthresh) perl $filtercon acd $filtercon 10 perl (defined $value && $value != $vdef)? " -conthresh=$value" : "" 9 conpath Location of contact files for input (-conpath) acd @(!$(randomise)) /data/contacts/ perl ($value && $value ne $vdef)? " -conpath=$value" : "" 10 conextn Extension of contact files (-conextn) acd @(!$(randomise)) .con perl ($value && $value ne $vdef)? " -conextn=$value" : "" 11 cpdbpath Location of coordinate files for input (embl-like format) (-cpdbpath) acd @(!$(randomise)) /data/cpdbscop/ perl ($value && $value ne $vdef)? " -cpdbpath=$value" : "" 12 cpdbextn Extension of coordinate files (embl-like format) (-cpdbextn) acd @(!$(randomise)) .pxyz perl ($value && $value ne $vdef)? " -cpdbextn=$value" : "" 13 filterpsim Ignore alignment postitions with post_similar value of 0 (-filterpsim) acd @(!$(randomise)) 0 perl ($value)? " -filterpsim" : "" 14 output output Section sigpath Location of signature files for output (-sigpath) ./ perl " -sigpath=$value" 15 sigextn Extension of signature files for output (-sigextn) .sig perl " -sigextn=$value" 16 auto perl " -auto -stdout" 17