showseq European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/display.showseq http://www.ebi.ac.uk/soaplab/emboss4/services/display.showseq?wsdl Displays a protein or a nucleic acid sequence in a style suitable for publication. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/showseq.html showseq Displays a protein or a nucleic acid sequence in a style suitable for publication. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/showseq.html sequence_usa Type: string. Any valid sequence with gaps. 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. Any valid sequence with gaps. 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#biological_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 format Type: string. Things to display. The allowed values (integers) for this parameter are: 0 (Enter your own list of things to display) | 1 (Sequence only) | 2 (Default sequence with features)| 3 (Pretty sequence) | 4 (One frame translation) | 5 (Three frame translations) | 6 (Six frame translations) | 7 (Restriction enzyme map) | 8 (Baroque). The default value is 2. This is a mandatory parameter. 2 false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter things_S Type: boolean. Display sequence. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_B Type: boolean. Display blank line. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_1 Type: boolean. Display frame1 translation. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_2 Type: boolean. Display frame2 translation. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_3 Type: boolean. Display frame3 translation. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_-1 Type: boolean. Display CompFrame1 translation. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_-2 Type: boolean. Display CompFrame2 translation. False by default.This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_-3 Type: boolean. Display CompFrame3 translation. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_T Type: boolean. Display tick line. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_N Type: boolean. Display number ticks line. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_C Type: boolean. Display complement sequence. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_F Type: boolean. Display features. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_R Type: boolean. Display restriction enzyme cut sites in forward sense. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_-R Type: boolean. Display restriction enzyme cut sites in reverse sense. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter things_A Type: boolean. Display annotation. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter translate Type: string. Regions to translate (if translating). If this is left blank 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 This is an optional parameter. 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 annotation Type: string. Regions to annotate by marking. If this is left blank, then no annotation is added. A set of regions is specified by a set of pairs of positions followed by optional text. The positions are integers. They are followed by any text (but not digits when on the command-line). Examples of region specifications are: 24-45 new domain 56-78 match to Mouse 1-100 First part 120-156 oligo. A file of ranges to annotate (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 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'. Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. The default value is all. This is an optional parameter. all 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 matchsource Type: string. By default any feature source in the feature table is shown. You can set this parameter to match any feature source you wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|', eg: gene* | embl. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchtype Type: string. By default any feature type in the feature table is shown. You can set this parameter to match any feature type you wish to show. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types. The type may be wildcarded by using '*'. If you wish to show more than one type, separate their names with the character '|', eg: *UTR | intron. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchsense Type: long. By default any feature type in the feature table is shown. You can set this parameter to match any feature sense you wish to show. 0 for any sense | 1 for forward sense | -1 for reverse sense. The default value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter minscore Type: float. Minimum score of feature to display. The default value is 0.0. This is an optional parameter. 0.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter maxscore Type: float. Maximum score of feature to display. Default value is 0.0. This is an optional parameter. 0.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchtag Type: string. Tag of feature to display. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. By default any feature tag in the feature table is shown. You can set this parameter to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|', eg: gene | label. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchvalue Type: string. Tag values are the values associated with a feature tag. Only some tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this parameter to match any feature tag value you wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with the character '|'. For example: pax* | 10. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter stricttags Type: boolean. By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this parameter is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed. This is an optional parameter. false 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. The default value is "false". This is an optional parameter. false 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 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 an optional parameter. 4 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. The default value is 'false'. 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. True by default. 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. True by default. 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. 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 this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered. false by default. This is anoptional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter commercial Type: boolean. Only use restriction enzymes with suppliers. True by default. This is an optional parameter. true 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. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them. The default vaulue 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 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. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter width Type: long. You can expand (or contract) the width of the ASCII-character graphics display of the positions of the features using this value. For example, a width of 80 characters would cover a standard page width and a width of 10 characters would be nearly unreadable. If the width is set to less than 4, the graphics lines and the scale line will not be displayed. This is an optional parameter. The default value is 60. 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. 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 features, translation etc.. false http://www.mygrid.org.uk/ontology#biological_sequence String http://www.mygrid.org.uk/ontology#displaying Soaplab service