emma European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma?wsdl Performs a multiple alignment of nucleic acid or protein sequences using ClustalW program. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/emma.html emma Performs a multiple alignment of nucleic acid or protein sequences using ClustalW program. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/emma.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. Any valid sequence. Choose this parameter if you want to provide the'sequence'value as string (nucleotide or protein sequence). 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 onlydend Type: string. Only produce dendrogram file. Default value is set to "No". This is an optional parameter. N false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter dend Type: string. Do alignment using an old dendrogram. The default value is set to "No". This is an optional parameter. N false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter dendfile_direct_data Type: string. Dendrogram (tree file) from clustalw. This is a optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter dendfile_url Type: string. Dendrogram (tree file) from clustalw. This is a optional parameter false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pwmatrix Type: string. The scoring table which describes the similarity of each amino acid to each other. There are 3 'in-built' series of weight matrices offered. Each consists of several matrices which work differently at different evolutionary distances. The allowed values for this parameter are: b, p, g, i, o. The default value is 'b'(blosum). This is an optional parameter. b false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pwdnamatrix Type: string. The scoring table which describes the scores assigned to matches and mismatches. The allowed values for this parameter are: i, c, o. The default value is 'i' (iub). This is an optional parameter. i false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pairwisedatafile_direct_data Type: string. Comparison matrix. This is a optional parameter false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pairwisedatafile_url Type: string. Comparison matrix. This is a optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matrix Type: string. This gives a menu where you are offered a choice of weight matrices. The default for proteins is the PAM series.There are 3 'in-built'series of weight matrices offered. Each consists of several matrices which work differently at different evolutionary distances. The allowed values for this parameter are: b, p, g, i, o. This is an optional parameter. b false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter dnamatrix Type: string. This gives a menu where a single matrix (not a series) can be selected. The allowed values for this parameter are: i, c, o. The default value is 'i'. This is an optional parameter i false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mamatrixfile_direct_data Type: string. Comparison matrix. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mamatrixfile_url Type: string. Comparison matrix file. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter slow Type: Boolean. A distance is calculated between every pair of sequences and these are used to construct the dendrogram which guides the final multiple alignment. The scores are calculated from separate pairwise alignments. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate). The slow-accurate method is fine for short sequences but will be VERY SLOW for many long (e.g.>1000 residue). The default value is set to the first method (dynamic programming).This is an optional parameter. Y false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pwgapopen Type: float. The penalty for opening a gap in the pairwise alignments. This is an optional parameter. 10.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter pwgapextend Type: float. The penalty for extending a gap by 1 residue in the pairwise alignments.Default value is 0.1. This is an optional parameter. 0.1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter ktup Type: long. This is the size of exactly matching fragment that is used. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity. For longer sequences (e.g.>1000 residues). Default value 1 for proteins, 2 for DNA. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapw Type: long. This is a penalty for each gap in the fast alignments. It has little affect on the speed or sensitivity except for extreme values. Default value is 3 for protein, 5 for DNA. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter topdiags Type: long. The number of k-tuple matches on each diagonal (in an imaginary dot-matrix plot). Only the best ones are used in the alignment. This parameter specifies how many. Decrease for speed; increase for sensitivity. Default value is 5 for protein, 4 for DNA. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter window Type: long. This is the number of diagonals around each of the 'best' diagonals that will be used. Decrease for speed; increase for sensitivity. Default value is 5 for protein, 4 for DNA. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter nopercent Type: boolean. Fast pairwise alignment: similarity scores: suppresses percentage score. Default value is 'No'. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapopen Type: float. The penalty for opening a gap in the alignment. Increasing the gap opening penalty will make gaps less frequent. The default value is 10.0. This is an optional parameter. 10.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapextend Type: float. The penalty for extending a gap by 1 residue. Increasing the gap extension penalty will make gaps shorter. The default value is 5.0. This is an optional parameter. 5.0 String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter endgaps Type: boolean. End gap separation: treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close. This is useful when you wish to align fragments where the end gaps are not biologically meaningful. The default value is 'true'. This is an optional parameter. true String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapdist Type: long. Gap separation distance: tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. This does not prevent close gaps; it makes them less frequent,promoting a block-like appearance of the alignment. The default value is 8.0. This is an optional parameter. 8 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter norgap Type: boolean. Residue specific penalties: amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine. The default value is "false". This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter hgapres Type: string. This is a set of the residues'considered'to be hydrophilic. It is used when introducing Hydrophilic gap penalties. Default value"GPSNDQEKR". This is a optional parameter. GPSNDQEKR false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter nohgap Type: boolean. Hydrophilic gap penalties: used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common. The residues that are'considered'to be hydrophilic are set by'-hgapres'parameter. The default value is "false".This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter maxdiv Type: long. This switch, delays the alignment of the most distantly related sequences until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical than this level to any other sequences will be aligned later. The default value is 30. This is an optional parameter. 30 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter osformat Type: string. Format of the output sequence (outseq). 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. 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 http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. false String dendoutfile Type: string. Dendrogram from clustalw outputfile. false String outseq Returns a multiple sequence alignment report. false http://www.mygrid.org.uk/ontology#multiple_sequence_alignment_report String http://www.mygrid.org.uk/ontology#multiple_local_aligning Soaplab service