sixpack European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/display.sixpack http://www.ebi.ac.uk/soaplab/emboss4/services/display.sixpack?wsdl Display a DNA sequence with 6-frame translation and ORFs. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/sixpack.html sixpack Display a DNA sequence with 6-frame translation and ORFs. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/sixpack.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 asequence_direct_data parameter but not both together. Parameter mandatory if the asequence_direct_data parameter hasn't been chosen. false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter sequence_direct_data Type: string. DNA seuqence. Choose this parameter if you want to provide the 'sequence' value as string. 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 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 witht he 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 table Type: string. Genetic codes. Enter the genetic code number. 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 value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter firstorf Type: boolean. Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter lastorf Type: boolean. Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mstart Type: boolean. Displays only ORFs starting with an M (Methionine). False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter reverse Type: boolean. Display also the translation of the DNA sequence in the 3 reverse frames. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter orfminsize Type: long. Minimum size of Open Reading Frames (ORFs) to display in the translations. The default value is 1. This is an optional parameter. 1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter uppercase Type: string. Regions to put in uppercase. If this is left blank, then the sequence case is left alone. 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 This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter highlight Type: string. Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red. A file of ranges to colour (one range per line) can be specified as '@filename'. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter number Type: boolean. Number the sequence at the beginning and the end of each line. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter width Type: long. Number of nucleotides displayed on each line. The default value is 60. This is an optional parameter. 60 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter length Type: long. Line length of page (0 for indefinite). The default value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter margin Type: long. Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number<1.0 or>1.0 to decrease or increase the size, respectively. The default value is 10. This is an optional parameter. 10 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter name Type: boolean. Set this to be false if you do not wish to display the ID name of the sequence. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter description Type: boolean. Set this to be false if you do not wish to display the description of the sequence. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter offset Type: long. Number from which you want the DNA sequence to be numbered. The default value is 1. This is an optional parameter. 1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter html Type: boolean. If you are sending the output to a file, this will format it for displaying as a table in a WWW document. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter osformat Type: string. Format for: ORF sequence output. 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 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 outfile Type: string. If you enter the name of a file here then this program will write the sequence details into that file. false String outseq Returns DNA sequence with 6-frame translation and ORFs. false http://www.mygrid.org.uk/ontology#nucleotide_sequence String http://www.mygrid.org.uk/ontology#translating http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service