1.2.1b lspread seq/db (LArge Scale Sequence compArison Package) Glemet, Codani lspread_seqdb lspread_seqdb perl "lspread" 0 queryname perl "/local/gensoft/lib/LASSAP/pasteur/majcmd.pl $cmdfile $query;" -10 lspextendrun perl ($lspextend)? "lspextend $infile;" : "" -5 do_lspread Save results for further analysis (lspread) perl "" 0 898 dumpfile perl " -dump results" results 900 perl $do_lspread lspcalc_result perl 1 lspcalc_result dumpcmdfile=cmdfile query sequences_file dumpcmdfile perl "" "$dumpfile.cmd" 899 perl $do_lspread flag_www perl " -www " 4000 perl $_html && ! $do_lspread && ! $sequences_file htmloutput perl " > results.html" "results.html" 5500 perl $_html && ! $do_lspread && ! $sequences_file display_options Display options 1000 view_alignment View alignment (-a) perl ($value)? " -a" : "" 0 1000 sort Sort options (-sort) perl ($value)? " -sort $value" : "" 800 SCORE Sort by Score PVAL Sort by Probability EXPECT Sort by Expect BY_ID Sort by lassap ID LENGTH Sort by Length ID_POS Sort by Percentage of Positive ID_STR Sort by Percentage of Indentities no message perl ( ($value eq "LENGTH" || $value eq "ID_POS" || $value eq "ID_STR" ) && ($lspextend=1) && 0) sl Show length of sequences in compacted form (-sl) perl ($value)? " -sl" : "" 0 1000 sm Show mutations (produce FT lines) (-sm) perl ($value)? " -sm" : "" 0 1000 Only supported currently with KERR and BLERR algorithms. dh Display Headers with alignments (-dh) perl ($value)? " -dh" : "" 0 1000 pretty_print Pretty print of headers perl ($value)? " -dh | sed \\"s/#/# /g\\" | tr \\"#\\" \\"\\n\\" " : "" 0 5000 perl !$do_lspread selection_options Selection options 530 bc Boolean connector for selection perl "" & 490 | |: OR & &: AND not_HD NOT perl "" 530 no message perl $not_HD && ($not_HD_s = "\\!") && 0 HD Select string in database header (HD) perl "" 530 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 "" > 530 < < <= <= = = >= >= > > 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 "" 530 RP_op Probability selection operator (RP) perl "" <= 530 <= <= = = >= >= > > 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 "" 530 RE_op Expect selection operator (RE) perl "" < 530 < < <= <= = = >= >= > > 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 "" 530 RI_op Identities selection operator (RI) perl "" > 530 < < <= <= = = >= >= > > 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 "" 530 RM_op Positive Matches operator (RM) perl "" > 530 < < <= <= = = >= >= > > 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 "" 530 RL_op Alignment Length selection operator (RL) perl "" > 530 < < <= <= = = >= >= > > 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 "" 530 OBQ_op Offset Begin Query operator (OBQ) perl "" 530 < < <= <= = = >= >= > > 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 "" 530 OEQ_op Offset End Query operator (OEQ) perl "" 530 < < <= <= = = >= >= > > 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 "" 530 OBD_op Offset Begin Database operator (OBD) perl "" 530 < < <= <= = = >= >= > > 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 "" 530 OED_op Offset End Database operator (OED) perl "" 530 < < <= <= = = >= >= > > 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 "" 530 SLD_op Sequence length selection operator (SLD) perl "" 530 < < <= <= = = >= >= > > 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 "" 530 SLQ_op Sequence length selection operator (SLQ) perl "" 530 < < <= <= = = >= >= > > 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 query (SLQ) perl "" 530 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 $SLA SLA Select on sequence length in both database and query (SLA) perl "" 530 read_flag_selection perl ($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 $prosite_lspread clustering_options Clustering options 1500 sf Build clusters using Single Linkage Clustering (-sf) perl ($value) ? " -sf" : "" 0 1500 perl ! $sF sF Build clusters using Single Linkage Clustering and save the result in a Fasta file (-sF) perl ($value) ? " -sF" : "" 0 1500 fasta_fam perl $sF Fam*.seq seqsfile perl $sF lspcalc_files lspcalc files infile lspcalc result file (-o option) perl " $value" 10 lspcalc_result perl 1 lspcalc_result cmdfile query cmdfile lspcalc command file (*.cmd) perl "" 10 query Query sequence perl "" -20