getPrimer Virginia Bioinformatics Institute http://pathport.bioinformatics.vt.edu:6565/axis/services/probedesign http://www.vbi.vt.edu/~pathport/services/wsdls/beta/probedesign.wsdl Analyzes a DNA sequence and chooses optimal primers for polymerase chain reaction (PCR), DNA sequencing, and hybridization probes for microarray experiments. getPrimer <s:arbitrarywsdl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:wsdl>http://www.vbi.vt.edu/~pathport/services/wsdls/beta/probedesign.wsdl</s:wsdl><s:operation>getPrimer</s:operation></s:arbitrarywsdl> Analyzes a DNA sequence and chooses optimal primers for polymerase chain reaction (PCR), DNA sequencing, and hybridization probes for microarray experiments. in0:sequence_id getPrimerRequest Sequence id or simple word to describe your sequence. For example: normal_sequence false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in1:sequence_target getPrimerRequest Sequence url, sequence string (DNA) or sequence file attachment. No format required false http://www.mygrid.org.uk/ontology#DNA_sequence String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in2:included_region getPrimerRequest Optional parameter. A sub-region of the given sequence in which to pick primers For example 20,400: only pick primers in the 400 base region starting at position 20 false http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter in3:target getPrimerRequest Optional parameter. A simple sequence repeat site or a single-base-pair polymorphism. The value should be a space-separated list of start and length pairs. For example: 50,2 requires primers to surround the 2 bases at positions 50 and 51 false http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter in4:excluded_region getPrimerRequest Optional parameter. A sub-region of the given sequence in which not to include in picked primers. For example: 401,7 forbids selection of primers in the 7 bases starting at 401 false http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter in5:primer_start_codon_position getPrimerRequest Index of the first base of a start codon. For example: -1000000 -1000000 false http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter in6:primer_opt_tm getPrimerRequest Optimum melting temperature(Celsius) for a primer oligo. For example 60.0 60.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in7:primer_min_tm getPrimerRequest Minimum acceptable melting temperature(Celsius) for a primer oligo. For example 57.0 57.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in8:primer_max_tm getPrimerRequest Maximum acceptable melting temperature(Celsius) for a primer oligo. For example 63.0 63.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in9:primer_max_diff_tm getPrimerRequest Maximum acceptable (unsigned) difference between the melting temperatures of the left and right primers. For example 100 100 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in10:primer_opt_size getPrimerRequest Optimum length (in bases) of a primer oligo. For example 20 20 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in11:primer_min_size getPrimerRequest Minimum acceptable length of a primer. Must be greater than 0 and less than or equal to primer_max_size. For example 18 18 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in12:primer_max_size getPrimerRequest Maximum acceptable length (in bases) of a primer. Currently this parameter cannot be larger than 35. 27 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in13:primer_gc_clamp getPrimerRequest Specified number of consecutive Gs and Cs at the 3'end of both the left and right primer. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in14:primer_min_gc getPrimerRequest Minimum allowable percentage of Gs and Cs in any primer. For example 20.0 20.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in15:primer_opt_gc_percent getPrimerRequest Optimal percentage of Gs and Cs in any primer. For example 50.0 50.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in16:primer_max_gc getPrimerRequest Maximum allowable percentage of Gs and Cs in any primer.For example 80.0 80.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in17:primer_salt_conc getPrimerRequest The millimolar concentration of salt (usually KCl) in the PCR. For example 50.0 50 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in18:primer_dna_conc getPrimerRequest The nanomolar concentration of annealing oligos in the PCR. For example 50.0 50.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in19:primer_num_ns_accepted getPrimerRequest Maximum number of unknown bases (N) allowable in any primer. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in20:primer_max_poly_x getPrimerRequest The maximum allowable length of a mononucleotide repeat, for example AAAAAA. For example 5 5 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in21:primer_first_base_index getPrimerRequest The index of the first base in the input sequence. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in22:primer_num_return getPrimerRequest The maximum number of primer pairs to return. For example 5 5 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in23:primer_max_end_stability getPrimerRequest The maximum stability for the five 3'bases of a left or right primer. For example 100 100 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in24:primer_self_any getPrimerRequest The maximum allowable local alignment score when testing a single primer for (local) self-complementarity and the maximum allowable local alignment score when testing for complementarity between left and right primers. Local self-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self-priming in the PCR. For example 8.00 8.00 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in25:primer_self_end getPrimerRequest The maximum allowable 3'-anchored global alignment score when testing a single primer for self-complementarity, and the maximum allowable 3'-anchored global alignment score when testing for complementarity between left and right primers. The 3'-anchored global alignment score is taken to predict the likelihood of PCR-priming primer-dimers. For example 3.00 3.00 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in26:primer_sequence_quality getPrimerRequest Optinal parameter. Sequence quality. List of space separated integers. There must be exactly one integer for each base in sequence if this argument is non-empty. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter in27:primer_min_quality getPrimerRequest The minimum sequence quality allowed within a primer. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in28:primer_min_end_quality getPrimerRequest The minimum sequence quality allowed within the 5'pentamer of a primer. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in29:primer_quality_range_min getPrimerRequest The minimum legal sequence quality. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in30:primer_quality_range_max getPrimerRequest The maximum legal sequence quality. For example 100 100 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in31:primer_product_opt_tm getPrimerRequest The optimum melting temperature for the PCR product.For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in32:primer_product_max_tm getPrimerRequest The maximum allowed melting temperature of the amplicon. For example 1000000.0 1000000.0 false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in33:primer_product_min_tm getPrimerRequest The minimum allowed melting temperature of the amplicon. For example -1000000.0 -1000000.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in34:primer_product_opt_size getPrimerRequest The optimum size for the PCR product. For example 0 0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in35:primer_product_size_range getPrimerRequest The associated values specify the lengths of the product that the user wants the primers to create, such as 100-150 200-250. 100-300 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in36:primer_penalty_wt_gt getPrimerRequest Penalty weight for primers with temperature over primer optimum melting temperature. For example 1.0 1.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in37:primer_penalty_wt_tm_lt getPrimerRequest Penalty weight for primers with temperature under primer optimum melting temperature. For example 1.0 1.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in38:primer_wt_size_lt getPrimerRequest Penalty weight for primers shorter than primer optimum length. For example 1.0 1.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in39:primer_wt_size_gt getPrimerRequest Penalty weight for primers longer than primer Optimum length. For example 1.0 1.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in40:primer_wt_gc_percent_lt getPrimerRequest Penalty weight for primers with GC percent less than primer optimal percentage of Gs and Cs. For example 1.0 1.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in41:primer_wt_gc_percent_gt getPrimerRequest Penalty weight for primers with GC percent greater than primer optimal percentage of Gs and Cs. For example 1.0 1.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in42:primer_wt_compl_any getPrimerRequest Penalty weight for primer local self-complementarity. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in43:primer_wt_compl_end getPrimerRequest Penalty weight for primer complementary end. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in44:primer_wt_num_ns getPrimerRequest Penalty weight for maximum number of unknown bases (N) allowable in any primer. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in45:primer_wt_seq_qual getPrimerRequest Penalty weight for primer sequence quality. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in46:primer_wt_end_qual getPrimerRequest Penalty weight for primer end quality. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in47:primer_wt_pos_qual getPrimerRequest Penalty weight for primer position quality. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in48:primer_wt_end_stability getPrimerRequest Penalty weight for primer_end_stability. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in49:primer_pair_wt_compl_any getPrimerRequest Penalty weight for alignment when testing inter-pair complementarity for the left and right primers. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in50:primer_pair_wt_compl_end getPrimerRequest Penalty weight for 3'-anchored global alignment when testing inter-pair complementarity for the left and right primers. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in51:primer_pair_wt_product_tm_gt getPrimerRequest Penalty weight for primer pair with PCR product temperature greater than primer product maximum temperature. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in52:primer_pair_wt_product_tm_lt getPrimerRequest Penalty weight for primer pair with PCR prodcut temperature less than primer product minimum temperature. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in53:primer_pair_wt_product_size_gt getPrimerRequest Penalty weight for primer pair with PCR prodcut size greater than primer product size range. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in54:primer_pair_wt_product_size_lt getPrimerRequest Penalty weight for primer pair with PCR prodcut size shorter than primer product size range. For example 0.0 0.0 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter getPrimerReturn getPrimerResponse Returns the list of available primers. false String http://www.mygrid.org.uk/ontology#predicting WSDL service