transeq European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq?wsdl Translate nucleic acid sequences to the corresponding peptide sequence. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/transeq.html transeq Translate nucleic acid sequences to the corresponding peptide sequence. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/transeq.html sequence_usa Type: string. Nucleotide 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 asequence_direct_data parameter but not both together. Parameter mandatory if the asequence_direct_data parameter has not been chosen. String sequence_direct_data Type: string. Nucleotide sequence. Choose this parameter if you want to provide the'sequence'value as string (nucleotide sequence). Parameter mandatory if the sequence_usa parameter hasn't been chosen. http://www.mygrid.org.uk/ontology#nucleotide_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. 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. String send Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end of the sequence. 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. 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. String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. String frame_1 Type: boolean(true/false). Translate forward frame 1. This is an optional parameter. The default is'true'. true String frame_2 Type: boolean(true/false). Translate forward frame 2. This is an optional parameter. The default is'false'. false String frame_3 Type: boolean(true/false). Translate forward frame 3. This is an optional parameter. The default is'false'. false String frame_F Type: boolean(true/false). Translate all 3 forward frames. This is an optional parameter. The default is'false'. false String frame_-1 Type: boolean(true/false). Translate reverse frame 1. This is an optional parameter. The default is'false'. false String frame_-2 Type: boolean(true/false). Translate reverse frame 2. This is an optional parameter. The default is'false'. false String frame_-3 Type: boolean(true/false). Translate reverse frame 3. This is an optional parameter. The default is'false'. false String frame_R Type: boolean(true/false). Translate all 3 reverse frames. This is an optional parameter. The default is'false'. false String frame_6 Type: boolean(true/false). Translate all 6 frames. This is an optional parameter. The default is'false'. 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 String regions Type: string. Regions to translate. If this is left blank, then the complete sequence is translated. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 Note: you should not try to use this option with any other frame than the default, frame=1. This is an optional parameter. String trim Type: boolean (true/false). This removes all'X'and'*'characters from the right end of the translation. The trimming process starts at the end and continues until the next character is not a'X'or a'*'. This is an optional parameter. The default is'false'. false String clean Type: boolean(true/false). This changes all STOP codon positions from the'*'character to'X'(an unknown residue). This is useful because some programs will not accept protein sequences with'*'characters in them. This is an optional parameter. The default is'false'. false String alternative Type: boolean. The default definition of frame'-1'is the reverse-complement of the set of codons used in frame 1. (Frame -2 is the set of codons used by frame 2, similarly frames -3 and 3). This is a common standard, used by the Staden package and other programs. If you prefer to define frame'-1'as using the set of codons starting with the last codon of the sequence, then set this to be true. This is an optional parameter. The default is'false'. false String osformat Type: string. Format of the output sequence (outseq). 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. The default value is'fasta'. fasta 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 outseq Returns peptide sequence false http://www.mygrid.org.uk/ontology#protein_sequence http://www.mygrid.org.uk/ontology#single_sequence_format String http://www.mygrid.org.uk/ontology#translating Soaplab service