showalign European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.showalign http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.showalign?wsdl Displays an aligned set of protein or a nucleic acid sequences 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/showalign.html showalign Displays an aligned set of protein or a nucleic acid sequences 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/showalign.html sequence_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 sequence_direct_data Type: string. The sequence alignment to be displayed. 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 matrix_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 matrix_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 refseq Type: string. If you give the number in the alignment or the name of a sequence, it will be used as the reference sequence. The reference sequence is always show in full and is the one against which all the other sequences are compared. By default the consensus sequence is used as the reference sequence. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter bottom Type: boolean. If this is true then the reference sequence is displayed at the bottom of the alignment as well as at the top. This is an optional parameter. true String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter show Type: string. What to show. The allowed values for this parameter are: A (for All of the sequences), I (for Identities between the sequences), N (for Non-identities between the sequences), S (for Similarities between the sequences), D (for Dissimilarities between the sequences). The default value is 'N'. This is an optional parameter. N false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter order Type: string. Output order of the sequences. The allowed values for this parameter are: I (for Input order - no change), A (for Alphabetical order of the names), S (for Similarity to the reference sequence). The default value is 'I'. This is an optional parameter I false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter similarcase Type: boolean. If this is set True, then when -show parameter is set to 'Similarities'(S) or 'Non-identities'(N) and a residue is similar but not identical to the reference sequence residue, it will be changed to lower-case. If the -show parameter is set to 'All'(A) then non-identical, non-similar residues will be changed to lower-case. If this is set False then no change to the case of the residues is made on the basis of their similarity to the reference sequence. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter consensus Type: boolean. If this is true then the consensus line is displayed. Default value is 'true'. This is an optional parameter. true 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 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. Default value is 'true'. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter ruler Type: boolean. If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed. Default value is 'true'. This is an optional parameter. true 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 margin Type: long. This sets the length of the left-hand margin for sequence names. If the margin is set at 0 then no margin and no names are displayed. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin. If the margin is set to -1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected. 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. Use HTML formatting. False by default. This is an optional parameter. false 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 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. 50.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter setcase Type: float. Sets the threshold for the scores of the positive matches above which the consensus is in upper-case and below which the consensus is in lower-case. By default this is set to be half of the (weight-adjusted) number of sequences in the alignment. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter identity Type: float. 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 0.0. This is an optional parameter. 0.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gaps Type: boolean. If this option is true then gap characters can appear in the consensus. The alternative is 'N' for nucleotide, or 'X' for protein. Default value is 'true'. This is an optional parameter. true 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 outfile Displays a multiple sequence alignment false http://www.mygrid.org.uk/ontology#multiple_sequence_alignment_report String http://www.mygrid.org.uk/ontology#displaying Soaplab service