prettyplot European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot?wsdl Reads in a set of aligned DNA or protein sequences and displays them graphically, with conserved regions highlighted in various ways (boxing and colouring). Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/prettyplot.html prettyplot Reads in a set of aligned DNA or protein sequences and displays them graphically, with conserved regions highlighted in various ways (boxing and colouring). Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/prettyplot.html sequences_usa Parameter type: String. 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 sequences_direct_data Type: string. Set of sequences 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 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 graph_format Type: string. Format of the graphical output. This is an optional parameter. The allowed values for this parameter are: png, postscript, colourps, hpgl. The default value is 'png'. png false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matrixfile_direct_data Type: string. This is the scoring matrix file used when comparing sequences. By default it is 'EBLOSUM62' (for proteins) or 'EDNAFULL' (for nucleic sequences). This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matrixfile_url Type: string. This is the scoring matrix file used when comparing sequences. By default it is 'EBLOSUM62' (for proteins) or 'EDNAFULL' (for nucleic sequences). This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter residuesperline Type: long. The number of residues to be displayed on each line. The default value is 50. This is an optional parameter. 50 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter resbreak Type: long. Number of residues before a space. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter ccolours Type: boolean. Colour residues by their consensus value. The default value is 'true'. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter cidentity Type: string. Colour to display identical residues. The default color is RED. This is an optional parameter. RED false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter csimilarity Type: string. Colour to display similar residues. The default colour is GREEN. This is an optional parameter. GREEN false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter cother Type: string. Colour to display other residues. The default value is BLACK. This is an optional parameter. BLACK false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter docolour Type: boolean. Colour residues by table oily, amide etc. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter shade Type: string. Set to BPLW(black, pale, light, white) for normal shading so for pair = 1.5,1.0,0.5 and shade = BPLW, Residues score Colour 1.5 or over... BLACK (B) | 1.0 to 1.5 ... BROWN (P) | 0.5 to 1.0 ... WHEAT (L) | under 0.5 .... WHITE (W). The only four letters allowed are BPLW, in any order. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pair Type: string. Values to represent identical similar related. EMBOSS known type: Three floating point threshold values for identical, similar and related residues. Default value: 1.5,1.0,0.5. This is an optional parameter. 1.5,1.0,0.5 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter identity Type: long. Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. The default value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter box Type: boolean. Display prettyboxes. Default value is set to true. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter boxcol Type: boolean. Colour the background in the boxes. The default value is set to false. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter boxcolval Type: string. Colour to be used for background. GREY is the default colour. This is an optional parameter. GREY false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter name Type: boolean. Display the sequence names. Default value is set to true. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter maxnamelen Type: long. Margin size for the sequence name. The default value is 10. This is an optional parameter. 10 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter number Type: boolean. Display the residue number. Default value is set to true. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter listoptions Type: boolean. Display the date and options used. Default value is 'true'. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter plurality Type: float. Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter consensus Type: boolean. Display the consensus. Default value is 'false'. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter collision Type: boolean. Allow collisions in calculating consensus. Default value is 'true'. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter alternative_0 Type: boolean. Normal collision check. Default value is 'true'. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter alternative_1 Type: boolean. Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. false by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter alternative_2 Type: boolean. If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 'false' is the default value. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter alternative_3 Type: boolean. Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. Default value is 'false'. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter showscore Type: long. Print residue scores. Default value is -1. This is an optional parameter. -1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter portrait Type: boolean. Set page to Portrait. The default value is 'false'. 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 Graphics_in_Postscript Returns a graphiacal representation of the alignment result in postscript format. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter Graphics Returns a graphiacal representation of the alignment result. false byte[] Graphics_in_PNG Returns a graphiacal representation of the alignment result in png format. false http://www.mygrid.org.uk/ontology#alignment_quality_graph byte[][] http://www.mygrid.org.uk/ontology#displaying Soaplab service