polydot European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_dot_plots.polydot http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_dot_plots.polydot?wsdl Displays all-against-all dotplots of a set of sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/polydot.html polydot Displays all-against-all dotplots of a set of sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/polydot.html sequences_usa Parameter type: string. The Uniform Sequence Address, or USA, is a standard way of specifying a sequence to be read into a program in EMBOSS. The most common ways of specifying a sequence is to type (database:entry), where database can be embl, uniprot or swissprot and entry is either the sequence`s entry or ID name, or its Accession number in that database. For example: database:accession =>embl:X65923 or swissprot:Q7M4G0| database:entry_name => swissprot:AMIC_PSEAE | database:ID_name => embl:paamir. Choose either this parameter or the asequence_direct_data parameter but not both together. Parameter mandatory if the asequence_direct_data parameter hasn't been chosen. false http://www.mygrid.org.uk/ontology#EMBL_accession String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter sequences_direct_data Type: string. File containing the sequences. Choose this parameter if you want to provide the 'sequences' value as string. Parameter mandatory if the sequences_usa parameter hasn't been chosen. false http://www.mygrid.org.uk/ontology#biological_sequence String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter sformat Type: string. Specifies the format of the input sequence. This is an optional parameter. The allowed values for this parameter are: gcg, gcg8, embl, swiss, fasta, ncbi, genbank, nbrf, pir, codata, strider, clustal, phylip, acedb, msf, jackknifer, jackknifernon, nexus, nexusnon, treecon, mega, meganon, ig, staden, text, raw. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sbegin Type: long. The first position to be used in the sequence, for example: sbegin=1 means start with the first base in the sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter send Type: long. The last position to be used in the sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter wordsize Type: long. The similar regions between the two sequences are found by creating a hash table of 'wordsize' subsequences. 10 is a reasonable default. Making this value larger (20?) may speed up the program slightly, but will mean that any two differences within 'wordsize' of each other will be grouped as a single region of difference. This value may be made smaller (4?) to improve the resolution of nearby differences, but the program will go much slower. This is a mandatory parameter. 6 false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter graph_format Type: string. Format of the graphical output. This is an optional parameter. The allowed values for this parameter are: png, postscript, colourps, hpgl, png false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gap Type: long. This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output. For example 10. This is an optional parameter. 10 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter boxit Type: boolean. Draw a box around each dotplot. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter dumpfeat Type: string. Dump all matches as feature files. This is an optional parameter. N false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter offormat Type: string. Format of the output features (outfeat). This is an optional parameter. The allowed values for this parameter are: embl, genbank, ddbj, gff, acedb, swissprot. gff false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter report Type: string. A general report for the underlying analysis job. false String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. false String outfeat Ouput features false String Graphics_in_Postscript Returns dotplot of given sequences in postscript false http://www.mygrid.org.uk/ontology#sequence_alignment_dot_plot String Graphics Returns dotplot of given sequences false byte[] Graphics_in_PNG Returns dotplot of given sequences in png false byte[][] http://www.mygrid.org.uk/ontology#displaying Soaplab service