infoalign European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.infoalign http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.infoalign?wsdl Retrieves information on a multiple sequence alignment. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/infoalign.html infoalign Retrieves information on a multiple sequence alignment. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/infoalign.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. Set of 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 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 provide the number in the alignment or the name of a sequence to this parameter, it will be used as the reference sequence. The reference sequence is the one against which all the other sequences are compared. If set to 0 then the consensus sequence will be used as the reference sequence. 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 plurality Type: float. Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is 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 identity Type: float. Set 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. Default value is 0.0. This is an optional parameter. 0.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter html Type: boolean. Format output as an HTML table. The default value is 'false'. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter only Type: boolean. This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount -noweight' to get only the sequence length output, you can specify '-only -seqlength'. Default value is false. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter heading Type: boolean. Display column headings. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter usa Type: boolean. Display the USA of the sequence. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter name Type: boolean. Display 'name' column. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter seqlength Type: boolean. Display 'seqlength' column. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter alignlength Type: boolean. Display 'alignlength' column. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gaps Type: boolean. Display number of gaps. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapcount Type: boolean. Display number of gap positions. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter idcount Type: boolean. Display number of identical positions. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter simcount Type: boolean. Display number of similar positions. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter diffcount Type: boolean. Display number of different positions. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter change Type: boolean. Display % number of changed positions. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter weight Type: boolean. Display 'weight' column. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter description Type: boolean. Display 'description' column. 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. String outfile Returns information on a multiple sequence alignment false http://www.mygrid.org.uk/ontology#multiple_sequence_alignment_report String http://www.mygrid.org.uk/ontology#retrieving Soaplab service