getProbe Virginia Bioinformatics Institute http://pathport.bioinformatics.vt.edu:6565/axis/services/yoda http://pathport.vbi.vt.edu/services/wsdls/beta/yoda.wsdl Analyses a DNA sequence and returns gene specific oligonucleotides probe. getProbe <s:arbitrarywsdl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:wsdl>http://pathport.vbi.vt.edu/services/wsdls/beta/yoda.wsdl</s:wsdl><s:operation>getProbe</s:operation></s:arbitrarywsdl> Analyses a DNA sequence and returns gene specific oligonucleotides probe. in0:design_file getProbeRequest File or URL containing sequences in fasta format. For example: http://staff.vbi.vt.edu/pathport//services/wsdls/NC_003318_10.ffn false http://www.mygrid.org.uk/ontology#DNA_sequence http://www.mygrid.org.uk/ontology#fasta_format String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in1:genome_file getProbeRequest Optional parameter. File containing genome sequences in fasta format. If genome file option is used, all sequences in design file must be in a genome file. false http://www.mygrid.org.uk/ontology#DNA_sequence http://www.mygrid.org.uk/ontology#fasta_format String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in2:host_file getProbeRequest Optional parameter. File containing sequences of host in fasta format. false http://www.mygrid.org.uk/ontology#DNA_sequence http://www.mygrid.org.uk/ontology#fasta_format String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in3:pseq getProbeRequest Prohibited sequences, each must be less than 16 bases. Or select "NONE" if there are not any prohibited sequences. NONE false http://www.mygrid.org.uk/ontology#DNA_sequence String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in4:oligoLength getProbeRequest Oligonucleotide length, an integer between 0 and 100. 60 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in5:revcompg getProbeRequest Reverse complement strands of genome sequence should be considered? Answer "YES" or "NO" NO false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in6:revcomph getProbeRequest Reverse complement strands of host sequence should be considered? Answer "YES" or "NO" false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in7:maxconshits getProbeRequest Maximum consecutive matches between oligo and another sequence, must be 14 or greater. For example 15 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in8:maxpercentid getProbeRequest Maximum percent identity between oligo and another sequence. For example 80. 80 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in9:maxpolyx getProbeRequest Maximum consecutive number of any base. For example 4 4 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in10:tmrange getProbeRequest Range of acceptable melting temperatures. For example 10.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in11:mintm getProbeRequest Minimum acceptable melting temperature, do not use with -tmrange. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in12:maxtm getProbeRequest Maximum acceptable melting temperature, do not use with -tmrange. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in13:dnaconc getProbeRequest DNA concentration (nM) for melting temperature calculation. For example 50.0 50.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in14:saltconc getProbeRequest Salt concentration (mM) for melting temperature calculation. For example 50.0 50.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in15:gcrange getProbeRequest Range of acceptable GC percentages, centered on average %GC. For example 10. 10 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in16:minGC getProbeRequest Minimum acceptable GC percentage, do not use with -gcrange 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in17:maxGC getProbeRequest Maximum acceptable GC percentage, do not use with -gcrange. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in18:dwindow getProbeRequest Dimer window length. For example 15 15 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in19:dstringency getProbeRequest Dimer stringency, number of matches within window. For example 14 14 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in20:hwindow getProbeRequest Hairpin window length (stem length). For example 7 7 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in21:hstringency getProbeRequest Hairpin stringency, number of matches within window. For example 7 7 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in22:hmingap getProbeRequest Minimum hairpin loop length. For example 3 3 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in23:hmaxgap getProbeRequest Maximum hairpin loop length. For example 6 6 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in24:mpps getProbeRequest Maximum Probes Per Sequence (used by Coverage Sorter). For example 1 1 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in25:probesorter getProbeRequest Sorter for probe. Select one of the following option: 3prime | 5prime | 5-middle-3 | middle | cover | nolap 3prime false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in26:rawseq getProbeRequest Show raw sequence? Answer "YES" or "NO" NO false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter getProbeReturn getProbeResponse Returns the set of probes false http://www.mygrid.org.uk/ontology#predicting WSDL service