fuzztran European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_motifs.fuzztran http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_motifs.fuzztran?wsdl Uses PROSITE style protein patterns to search nucleic acid sequences translated in the specified frame(s). Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/fuzztran.html fuzztran Uses PROSITE style protein patterns to search nucleic acid sequences translated in the specified frame(s). Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/fuzztran.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. false http://www.mygrid.org.uk/ontology#EMBL_accession 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 pattern Type: string. The standard IUPAC one-letter codes for the amino acids are used. The symbol `x' is used for a position where any amino acid is accepted. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses `[ ]'. For example: [ALT] stands for Ala or Leu or Thr. Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a gven position. For example: {AM} stands for any amino acid except Ala and Met. Each element in a pattern is separated from its neighbor by a `-'. (Optional in fuzztran) Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x. When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol. A period ends the pattern. (Optional in fuzztran). For example, [DE](2)HS{P}X(2)PX(2,4)C. This is a mandatory parameter. false String frame Type: string. Frame(s) to translate. This is an optional parameter. The allowed values for this parameter are: 1 (Forward 1)| 2 (Forward 2)| 3 (Forward 3)| F (Forward three frames)| -1 (Reverse 1)| -2 (Reverse 2)| -3 (Reverse 3)| R (Reverse three frames)| 6 (All six frames) The default is 1. 1 false String table Type: string. Genetics code used for the translation. This is an optional parameter. The allowed values for this parameter are: 0 (Standard)| 1 (Standard (with alternative initiation codons))| 2 (Vertebrate Mitochondrial)| 3 (Yeast Mitochondrial)| 4 (Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)| 5 (Invertebrate Mitochondrial)| 6 (Ciliate Macronuclear and Dasycladacean)| 9 (Echinoderm Mitochondrial)| 10 (Euplotid Nuclear)| 11 (Bacterial)| 12 (Alternative Yeast Nuclear)| 13 (Ascidian Mitochondrial)| 14 (Flatworm Mitochondrial)| 15 (Blepharisma Macronuclear)| 16 (Chlorophycean Mitochondrial)| 21 (Trematode Mitochondrial)| 22 (Scenedesmus obliquus)| 23 (Thraustochytrium Mitochondrial) The default is 0. 0 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 the number of matches found with their start and end position. false String http://www.mygrid.org.uk/ontology#searching http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service