remap European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/display.remap http://www.ebi.ac.uk/soaplab/emboss4/services/display.remap?wsdl Display sequence with restriction sites,translation etc. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/remap.html remap Display sequence with restriction sites,translation etc. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/remap.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 String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter sequence_direct_data Type: string. DNA sequence. Choose this parameter if you want to provide the'sequence'value as string (DNA squence). Parameter mandatory if the sequence_usa parameter hasn't been chosen. false http://www.mygrid.org.uk/ontology#nucleotide_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 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 enzymes Type: string. The name'all'reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as:'HincII,hinfI,ppiI,hindiii'. The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a'@'character in front of it, for example,'@enz.list'. The default value is"all". This is an optional parameter. all false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sitelen Type: long. This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. The default value is 4. This is a mandatory parameter. 4 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mincuts Type: long. This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored. The default value is 1. This is an optional parameter. 1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter maxcuts Type: long. This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored. The default value is 2000000000. This is an optional parameter. 2000000000 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter single Type: boolean. If this is set then it forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter blunt Type: boolean. This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. The default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sticky Type: boolean. This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. The default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter ambiguity Type: boolean. This allows those enzymes which have one or more'N'ambiguity codes in their pattern to be considered. The default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter plasmid Type: boolean. If this is set then it allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered. The default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter commercial Type: boolean. If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through'all'the enzymes in the REBASE database. The default value is"true". This is an optional parameter. true 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 frame_1 Type: boolean. Translate frame 1. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_2 Type: boolean. Translate frame 2. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_3 Type: boolean. Translate frame 3. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_F Type: boolean. Translate Forward three frames. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_-1 Type: boolean. Translate Reverse frame 1. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_-2 Type: boolean. Translate Reverse frame 2. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_-3 Type: boolean. Translate Reverse frame 3. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_R Type: boolean. Translate Reverse three frames. Default value is"false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter frame_6 Type: boolean. Translate all 6 frames. Default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter cutlist Type: boolean. This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut. The default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter flatreformat Type: boolean. This changes the output format to one where the recognition site is indicated by a row of'==='characters and the cut site is pointed to by a'>'character in the forward sense, or a'<'in the reverse sense strand. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter limit Type: boolean. This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching'all'of them. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter translation Type: boolean. This displays the 6-frame translations of the sequence in the output. The default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter reverse Type: boolean. This displays the cut sites and translation of the reverse sense. The default value is"true". This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter orfminsize Type: long. This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to'-'characters. The default value is 0. This is an optional parameter. 0 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 specifed as'@filename'. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter threeletter Type: boolean. Display protein sequences in three-letter code. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter number Type: boolean. If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment. The default value is'false'. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter width Type: long. Width of sequence to display. 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. Offset to start numbering the sequence from. 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 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 Returns sequence with restriction sites,translation etc. false http://www.mygrid.org.uk/ontology#REBASE_record String http://www.mygrid.org.uk/ontology#predicting http://www.mygrid.org.uk/ontology#REBASE Soaplab service