ehmmsearch European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/hmm.ehmmsearch http://www.ebi.ac.uk/soaplab/emboss4/services/hmm.ehmmsearch?wsdl Search a sequence database with a profile HMM. Detailed info about this operation can be found at the following links: http://web.mit.edu/emboss_v4.0.0/www/embassy/hmmernew/ehmmsearch.html and http://www.csb.yale.edu/userguides/seq/hmmer/docs/ ehmmsearch Search a sequence database with a profile HMM. Detailed info about this operation can be found at the following links: http://web.mit.edu/emboss_v4.0.0/www/embassy/hmmernew/ehmmsearch.html and http://www.csb.yale.edu/userguides/seq/hmmer/docs/ seqfile_usa Type: string. File of input 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 seqfile_direct_data parameter but not both together. Parameter mandatory if the seqfile_direct_data parameter has not been chosen. false String seqfile_direct_data Type: string. File of input 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 http://www.mygrid.org.uk/ontology#single_sequence_format String 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 a Type: long. Limits the alignment output to the<n>best scoring domains. a=0 shuts off the alignment output and can be used to reduce the size of output files. This is a mandatory parameter. The default value is 100. 100 false String e Type: float. Set the E-value cutoff for the per-sequence ranked hit list to<x>, where<x>is a positive real number. The default value is 10.0. Hits with E-values better than (less than) this threshold will be shown. This is an optional parameter. 10.0 false String t Type: float. Set the bit score cutoff for the per-sequence ranked hit list to<x>, where<x>is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown. This is an optional parameter. -1000000.0 false String z Type: long. Calculate the E-value scores as if we had seen a sequence database of<n>sequences. The default is the number of sequences seen in your database file<seqfile>. This is an optional parameter. false String compat Type: boolean. Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don't have to be rewritten. This is an optional parameter. The default value is'false'. false false String cpu Type: long. Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems). This is an optional parameter. false String cutga Type: boolean. Use Pfam GA (gathering threshold) score cutoffs. hmmbuildputs these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file,'cutga'parameter doesn't work. This is an optional parameter. The default value is'false'. false false String cuttc Type: boolean. Use Pfam TC (trusted cutoff) score cutoffs. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. This is an optional parameter. The default value is'false'. false false String cutnc Type: boolean. Use Pfam NC (noise cutoff) score cutoffs. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. This is an optional parameter the default value is'false'. false false String dome Type: float. Set the E-value cutoff for the per-domain ranked hit list to<x>, where<x>is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. This is an optional parameter. 1000000.0 false String domt Type: float. Set the bit score cutoff for the per-domain ranked hit list to<x>, where<x>is a real number. The default is negative infinity; by default, all domains in the sequences that passed the first threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. This is an optional parameter. -1000000.0 false String forward Type: boolean. Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. This is an optional parameter. The default value is'false'. false false String nulltwo Type: boolean. Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. This is an optional parameter. The default value is'false'. false false String pvm Type: boolean. Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile. gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for'pvm'parameter to function. This is an optional parameter. The default value is'false'. false false String xnu Type: boolean. Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. 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 outfile The output consists of four sections: a ranked list of the best scoring sequences, a ranked list of the best scoring domains, alignments for all the best scoring domains, and a histogram of the scores. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and bit score thresholds may also be applied to the domain list using the 'dome' and 'domt' parameters options. false http://www.mygrid.org.uk/ontology#pairwise_sequence_alignment_report String http://www.mygrid.org.uk/ontology#pairwise_local_aligning Soaplab service