1.2.1b check results against prosite (LArge Scale Sequence compArison Package) Glemet, Codani lspcalc_prosite lspcalc_prosite perl "/local/gensoft/lib/LASSAP/pasteur/Lsprebank.pl -r $infile -n resultsdb" 0 prosite_lspcalc 1 lspread Save results for further analysis (lspread) perl "" 1 998 lspread_flag_selection perl ($sel_options)? " -s \\"{ $sel_options }\\"" : "" 500 output_options Output options view_alignment View alignment (-a) perl ($value)? " -a" : "" 0 1000 Not available for all methods. scut Score cutoff (report results of scores greater than cutoff) (-scut) perl (defined $value)? " -scut $value" : "" 800 ecut Expect cutoff (Report results of expect values lower than cutoff) (-ecut) perl (defined $value)? " -ecut $value" : "" 800 max Maximum number of results reported (-max) perl (defined $value)? " -max $value" : "" 800 queryname perl "/local/gensoft/lib/LASSAP/pasteur/majcmd.pl $cmdfile $query;" -10 selection_options Results selection options bc Boolean connector for selection perl "" & 490 | |: OR & &: AND not_HD NOT perl "" no message perl $not_HD && ($not_HD_s = "\\!") && 0 HD Select string in database header (HD) perl "" Warning : for HD, in the current version, only ID field is scanned. This will be replaced by a full header scan, as implemented in database selections. no message perl $HD && ($hf="HD") && (($prosite_lspread && ($hf="HQ")) || 1) && (($HD_field && ($HD_field_s="# $HD_field")) || 1) && ($sel_options=($sel_options)? "($sel_options $bc ($not_HD_s $hf $HD_field_s $HD))" : "($not_HD_s $hf $HD_field_s $HD)") && 0 HD_field Type of database header (for HD) perl "" ID 520 all fields ID ID AC AC OS OS DE DE OC OC KW KW CL CL AL AL CC CC GN GN perl $HD RS_op Score selection operator (RS) perl "" > < < <= <= = = >= >= > > no message perl $RS && ($sel_options=($sel_options)? "($sel_options $bc RS $value $RS)" : "RS $value $RS") && 0 perl $RS RS Score selection value (RS) perl "" RP_op Probability selection operator (RP) perl "" <= <= <= = = >= >= > > no message perl $RP && ($sel_options=($sel_options)? "($sel_options $bc RP $value $RP)" : "RP $value $RP") && 0 perl $RP RP Probability selection value (RP) perl "" RE_op Expect selection operator (RE) perl "" < < < <= <= = = >= >= > > no message perl $RE && ($sel_options=($sel_options)? "($sel_options $bc RE $value $RE)" : "RE $value $RE") && 0 perl $RE RE Expect selection value (RE) perl "" RI_op Identities selection operator (RI) perl "" > < < <= <= = = >= >= > > no message perl $RI && ($sel_options=($sel_options)? "($sel_options $bc RI $value $RI)" : "RI $value $RI") && ($lspextend=1) && 0 perl $RI RI Select on Identities (RI) perl "" RM_op Positive Matches operator (RM) perl "" > < < <= <= = = >= >= > > no message perl $RM && ($sel_options=($sel_options)? "($sel_options $bc RM $value $RM)" : "RM $value $RM") && ($lspextend=1) && 0 perl $RM RM Select on Positive Matches (RM) perl "" RL_op Alignment Length selection operator (RL) perl "" > < < <= <= = = >= >= > > no message perl $RL && ($sel_options=($sel_options)? "($sel_options $bc RL $value $RL)" : "RL $value $RL") && ($lspextend=1) && 0 perl $RL RL Select on alignment Length (RL) perl "" OBQ_op Offset Begin Query operator (OBQ) perl "" < < <= <= = = >= >= > > no message perl $OBQ && ($sel_options=($sel_options)? "($sel_options $bc OBQ $value $OBQ)" : "OBQ $value $OBQ") && 0 perl $OBQ OBQ Offset Begin Query (OBQ) perl "" OEQ_op Offset End Query operator (OEQ) perl "" < < <= <= = = >= >= > > no message perl $OEQ && ($sel_options=($sel_options)? "($sel_options $bc OEQ $value $OEQ)" : "OEQ $value $OEQ") && 0 perl $OEQ OEQ Offset End Query (OEQ) perl "" OBD_op Offset Begin Database operator (OBD) perl "" < < <= <= = = >= >= > > no message perl $OBD && ($sel_options=($sel_options)? "($sel_options $bc OBD $value $OBD)" : "OBD $value $OBD") && 0 perl $OBD OBD Offset Begin Database (OBD) perl "" OED_op Offset End Database operator (OED) perl "" < < <= <= = = >= >= > > no message perl $OED && ($sel_options=($sel_options)? "($sel_options $bc OED $value $OED)" : "OED $value $OED") && 0 perl $OED OED Offset End Database (OED) perl "" SLD_op Sequence length selection operator (SLD) perl "" < < <= <= = = >= >= > > no message perl $SLD && ($sel_options=($sel_options)? "($sel_options $bc SLD $value $SLD)" : "SLD $value $SLD") && 0 perl $SLD SLD Select on sequence length in database (SLD) perl "" SLQ_op Sequence length selection operator (SLQ) perl "" < < <= <= = = >= >= > > no message perl $SLQ && ($sel_options=($sel_options)? "($sel_options $bc SLQ $value $SLQ)" : "SLQ $value $SLQ") && 0 perl $SLQ SLQ Select on sequence length in database (SLQ) perl "" SLA_op Sequence length selection operator (SLA) perl "" 547 < < <= <= = = >= >= > > no message perl $SLA && ($sel_options=($sel_options)? "($sel_options $bc SLA $value $SLA)" : "SLA $value $SLA") && 0 perl $SLA SLA Select on sequence length in both database and query (SLA) perl "" read_flag_selection perl ($sel_options)? " -pp \\"{ ($sel_options) }\\" " : "" 595 perl ! ($prosite_lspcalc || $prosite_lspread) prosite_flag_selection perl ($sel_options)? " -pp \\"{ (($sel_options) & ( ( (! HQ #ID _GLYCOSYLATION) & (! HQ #ID _PHOSPHO_SITE)) & (! HQ #ID MYRISTYL) ) )}\\" " : " -pp \\"{ ( ( (! HQ #ID _GLYCOSYLATION) & (! HQ #ID _PHOSPHO_SITE)) & (! HQ #ID MYRISTYL) ) }\\"" 595 perl $prosite_lspread prosite_options Prosite selection options db_bc Boolean connector for selection perl "" & | |: OR & &: AND all_fields All fields perl "" no message perl $all_fields && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc H $all_fields)" : "H $all_fields") && 0 ID ID perl "" no message perl $ID && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc H \\#ID $ID)" : "H \\#ID $ID") && 0 AC AC perl "" no message perl $AC && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc H \\#AC $AC)" : "H \\#AC $AC") && 0 not_OS NOT perl "" no message perl $not_OS && ($not_OS_s = "\\!") && 0 OS OS: organism perl "" no message perl $OS && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc ($not_OS_s H \\#OS $OS))" : "($not_OS_s H \\#OS $OS)") && 0 not_OC NOT perl "" no message perl $not_OC && ($not_OC_s = "\\!") && 0 OC OC: organism class perl "" no message perl $OC && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $bc ($not_OC_s H \\#OC $OC))" : "($not_OC_s H \\#OC $OC)") && 0 not_DE NOT perl "" no message perl $not_DE && ($not_DE_s = "\\!") && 0 DE DE: description perl "" no message perl $DE && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc ($not_DE_s H \\#DE $DE))" : "($not_DE_s H \\#DE $DE)") && 0 not_KW NOT perl "" no message perl $not_KW && ($not_KW_s = "\\!") && 0 KW KW: keyword perl "" no message perl $KW && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc ($not_KW_s H \\#KW $KW))" : "($not_KW_s H \\#KW $KW)") && 0 lengths_op sequences length operator perl "" < < <= <= = = >= >= > > no message perl $lengths && ($prosite_sel_options=($prosite_sel_options)? "($prosite_sel_options $db_bc L $lengths_op $lengths)" : "L $lengths_op $lengths") && 0 perl $lengths lengths sequences length (L) perl "" db_flag_selection perl ($prosite_sel_options)? " \\"{ " : "" 750 db_flag_selection2 perl ($prosite_sel_options)? " $prosite_sel_options }\\" " : "" 760 prosite_cmd perl " ; lspcalc -M PATT -db resultsdb -db prosite " 700 lspcalc_files lspcalc files infile lspcalc result file (-o option) perl "" 10 lspcalc_result perl 1 lspcalc_result cmdfile query cmdfile lspcalc command file (*.cmd) perl "" 10 query Query sequence perl "" -20 results_file perl " -o prosite_results" prosite_results 799 perl (! $view_alignment) && $lspread lspcalc_prosite_result perl 1 lspcalc_prosite_result outcmdfile=cmdfile resultsdb resultsdbseq resultsdbind resultsdbtab outcmdfile perl "" "$results_file.cmd" 701 perl $lspread resultsdb perl "" "resultsdb" 701 perl $lspread resultsdbseq perl "" "resultsdb.seq" 701 perl $lspread resultsdbind perl "" "resultsdb.ind" 701 perl $lspread resultsdbtab perl "" "resultsdb.tab" 701 perl $lspread