tcode European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_gene_finding.tcode http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_gene_finding.tcode?wsdl Tests DNA sequences for protein coding regions using an algorithm (Fickett TESTCODE) which looks for simple and universal differences between protein-coding and noncoding DNA. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/tcode.html tcode Tests DNA sequences for protein coding regions using an algorithm (Fickett TESTCODE) which looks for simple and universal differences between protein-coding and noncoding DNA. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/tcode.html sequence_usa Type: string. DNA sequence. 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 sequence_direct_data parameter but not both together. Parameter mandatory if the sequence_direct_data parameter has not been chosen. String sequence_direct_data Type: string. DNA sequence. Choose this parameter if you want to provide the 'sequence' value as string (DNA sequence). Parameter mandatory if the sequence_usa parameter hasn't been chosen. false http://www.mygrid.org.uk/ontology#DNA_sequence http://www.mygrid.org.uk/ontology#single_sequence_format String 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. By default the service autodetects the sequence format. false String sbegin Type: long. The first position to be used in the sequence, for example: sbegin=1 (default value) means start with the first base in the sequence. This is an optional parameter. false String send Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end the sequence. false String sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. By default the service can autodetect if a sequence is a nucleotide or protein sequence. false String snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. By default the service can autodetect if a sequence is a nucleotide or protein sequence. false String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. false String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. false String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. false String window Type: long. This is the number of nucleotide bases over which the TESTCODE statistic will be performed each time. The window will then slide along the sequence, covering the same number of bases each time. This is an optional parameter. The default is 200. 200 false String 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. The default is 'png'. png false String datafile_direct_data Type: string. The default data file is Etcode.dat and contains coding probabilities for each base. The probabilities are for both positional and compositional information. This is an optional parameter. false String datafile_url Type: string. The default data file is 'Etcode.dat' and contains coding probabilities for each base. The probabilities are for both positional and compositional information. This is an optional parameter. Etcode.dat false String step Type: long. The selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive). This may be altered to increase or decrease the increment of the slide. This is an optional parameter. The default is 3. 3 false String plot Type: boolean (Yes/No). On selection a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed. Sequence above the green line is coding, that below the red line is non-coding. This is an optional parameter. The default is 'No'. N false String report Type: string. A general report for the underlying analysis job. String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. String outfile Returns coding and non-coding region if the 'plot' parameter is set to 'no'. false String Graphics_in_Postscript Plot potential coding and non-coding region in postscript format if you select 'postcript' as 'graph_format' and set 'plot' parameter to 'yes'. false String Graphics byte[] Graphics_in_PNG Plot potential coding and non-coding region in png format if you select 'png' as 'graph_format' and set 'plot' parameter to 'yes'. false byte[][] http://www.mygrid.org.uk/ontology#displaying http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service