needle European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_global.needle http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_global.needle?wsdl Needleman-Wunsch global alignment. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/needle.html needle Needleman-Wunsch global alignment. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/needle.html asequence_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 asequence_direct_data Type: string. Any valid sequence. Choose this parameter if you want to provide the 'asequence' value as string. Parameter mandatory if the asequence_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 sformat1 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 sbegin1 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 send1 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 sprotein1 Type: boolean. Is the sequence a protein? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter snucleotide1 Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sreverse1 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 slower1 Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter supper1 Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter bsequence_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 bsequence_direct_data Type: string. Any valid sequence. Choose this parameter if you want to provide the 'bsequence' value as string. Parameter mandatory if the bsequence_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 sformat2 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 sbegin2 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 send2 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 sprotein2 Type: boolean. Is the sequence a protein? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter snucleotide2 Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sreverse2 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 slower2 Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter supper2 Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapopen Type: float. The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gapextend Type: float. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter datafile_direct_data Type: string. This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter datafile_url Type: string. This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter brief Type: boolean. Brief identity and similarity. This is an optional parameter. true 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 Return a sequence alignment report. false http://www.mygrid.org.uk/ontology#pairwise_sequence_alignment_report String http://www.mygrid.org.uk/ontology#pairwise_global_aligning Soaplab service