getGlimmers Virginia Bioinformatics Institute http://pathport.bioinformatics.vt.edu:6565/axis/services/glimmer http://www.vbi.vt.edu/~pathport/services/wsdls/beta/glimmer.wsdl Used to predict genes in genomic DNA sequences. It wraps GLIMMER(Gene Locator and Interpolated Markov ModelER) native program to analyzes genomic DNA sequences especially the genomes of bacteria and archaea by using interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The results of glimmer are returned using a subset of dasML format. getGlimmers <s:arbitrarywsdl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:wsdl>http://www.vbi.vt.edu/~pathport/services/wsdls/beta/glimmer.wsdl</s:wsdl><s:operation>getGlimmers</s:operation></s:arbitrarywsdl> Used to predict genes in genomic DNA sequences. It wraps GLIMMER(Gene Locator and Interpolated Markov ModelER) native program to analyzes genomic DNA sequences especially the genomes of bacteria and archaea by using interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The results of glimmer are returned using a subset of dasML format. in0:sequence_target getGlimmersRequest Nucleotide sequence in fasta format, url containing the sequence in fasta format or sequence file attachment. 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:self_training getGlimmersRequest Boolean value to determine if using sequence target as training sequence to build model. Select Yes or No Yes false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in2:add_training getGlimmersRequest Additional training sequence data provided to build model. Nucleotide sequence in fasta format, url containing the sequence in fasta format or sequence file attachment.Select"NONE"to avoid this process NONE 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:run_longorf getGlimmersRequest Boolean value to determine if using additional training sequences to run long orf (Open Reading Frame) to build potential genes list. Select"Yes"or"No" No false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in4:start_codon getGlimmersRequest Start codon to choose. 2 options available:"Use first codon in orf"or"Use Ribosome binding energy to choose" Use first codon in orf false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in5:genome_type getGlimmersRequest Specify whether the genome is circular or linear circular false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in6:auto_min_gene_len_training getGlimmersRequest Boolean value to determine if letting program compute the minimum gene length for training. Select"YES"or"NO". YES false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in7:user_min_gene_len_traning getGlimmersRequest user-provided minimum gene length for training (ignored if letting program compute). For example 500 500 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in8:auto_min_gene_len getGlimmersRequest Boolean value to determine if letting program compute the minimum gene length. Select"YES"or"NO" YES false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in9:user_min_gene_len getGlimmersRequest user-provided minimum predictive gene length (ignored if letting program compute). For example 100 100 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in10:min_overlap_len getGlimmersRequest Specify the minimum overlap length. For example 30 30 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in11:min_overlap_p getGlimmersRequest Specify the miminum overlap percentage. For example 10 10 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in12:indpscore getGlimmersRequest Boolean. Use independent probability score column. Select"YES"or"NO" YES false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in13:threshold getGlimmersRequest Specify the score for calling as gene. For example 90 90 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in14:auto_weakscore_len getGlimmersRequest Boolean value to determine if letting the program compute the n value to use"weak scores"on potential genes at least n bases long. Select"YES"or"NO" YES false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter in15:user_weakscore_len getGlimmersRequest User-provided n value to use weak scores on potential genes at least this number bases long (being ignored if letting program compute). For example 935 935 false http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter getGlimmersReturn getGlimmersResponse Returns the gene prediction info in xml format false http://www.mygrid.org.uk/ontology#gene_prediction_report XMLString http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter http://www.mygrid.org.uk/ontology#predicting http://www.mygrid.org.uk/ontology#gene_prediction_algorithm WSDL service