ehmmalign European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/hmm.ehmmalign http://www.ebi.ac.uk/soaplab/emboss4/services/hmm.ehmmalign?wsdl Align sequences to an HMM profile. Detailed info about this operation can be found at the following links: http://emboss.sourceforge.net/apps/release/4.1/embassy/hmmernew/ehmmalign.html and http://www.csb.yale.edu/userguides/seq/hmmer/docs/ ehmmalign Align sequences to an HMM profile. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.1/embassy/hmmernew/ehmmalign.html seqfile_usa Type: string. Set of sequences. 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 sequence_direct_data parameter but not both together. Parameter mandatory if the sequence_direct_data parameter has not been chosen. false String seqfile_direct_data Type: string. Set of sequences. Choose this parameter if you want to provide the'seqfile' value as string. Parameter mandatory if the seqfile_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. By default the program autodetects the sequence format. false String sbegin Type: long. The first position to be used in the sequence, for example: sbegin=1 (default value) means start with the first base in the sequence. This is an optional parameter. false String send Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end the sequence. false String sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. By default the program autodetects if a sequence is a nucleotide or protein sequence. false String snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. By default the program autodetects if a sequence is a nucleotide or protein sequence. false String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. false String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. false String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. false String hmmfile_direct_data Type: string. Specify the HMM profile. Parameter 'hmmfile_url' and' hmmfile_direct_data' are mutually exclusive. This is a mandatory parameter if 'hmmfile_url' parameter has not been selected. false String hmmfile_url Type: string. HMM profile. Parameter 'hmmfile_url' and 'hmmfile_direct_data' are mutually exclusive. This is a mandatory parameter if' hmmfile_direct_data' parameter has not been selected. false String mapali_direct_data Type: string. Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a'map'kept in the HMM, and so is fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. The alignment in the file must be exactly the alignment that the HMM was built from. This is a mandatory parameter if'mapali_url'parameter has not been selected. Parameter'mapali_url'and'mapali_direct_data'are mutually exclusive. false String mapali_url Type: string. Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a'map'kept in the HMM, and so is fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. The alignment in the file must be exactly the alignment that the HMM was built from. This is a mandatory parameter if'mapali_direct_data'parameter has not been selected. Parameter 'mapali_url' and 'mapali_direct_data' are mutually exclusive. false String withali_direct_data Type: string. Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). However, any alignment can be used, not just the alignment that the HMM was built from. This is a mandatory parameter if'withali_url'parameter has not been selected. Parameter'withali_url' and' withali_direct_data' are mutually exclusive. false String withali_url Type: string. Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). However, any alignment can be used, not just the alignment that the HMM was built from. This is a mandatory parameter if'withali_direct_data'parameter has not been selected. Parameter'withali_url'and'withali_direct_data'are mutually exclusive. false String m Type: boolean. Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. This is an optional parameter. The default value is'false'. false false String q Type: boolean. Quiet; suppress all output except the alignment itself. Useful for piping or redirecting the output. This is an optional parameter. The default value is'false'. false false String 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 output Multiple sequence alignment output false http://www.mygrid.org.uk/ontology#multiple_sequence_alignment_report String http://www.mygrid.org.uk/ontology#multiple_local_aligning Soaplab service