AnnotQTL Usage: Provide the annotation of a specific genomic region using several databases (NCBI, Ensembl, HGNC, GO, etc). Arguments: --taxon taxon_id define the species of interest by using the Taxon ID provided by NCBI. 9913 for Bos taurus 9615 for Canis familiaris 9796 for Equus caballus 9031 for Gallus gallus 9823 for Sus scrofa 7955 for Danio Rerio 10116 for Rattus norvegicus --chr name define the chromosome name --start location define the start location of the genomic region (in bases) --end location define the end location of the genomic region (in bases) --snp-file file (optionnal) SNP datafile to include in the annotation genomic window. File must have the following format SNP file chromosome location The first line of the file can be an header beginning with a '#'. A fourth column can be added in the file to display user-specific data (p-value, etc...). --snp-remap (optionnal) re-map SNP location using locations in dbSNP. If the SNP is not in the dbSNP, the location remains the same. --mp-keyword keyword (optionnal) define the keyword to be search in the Mammalian Phenotype database (i.e. reproductive). Several keywords can be added by seperating them with a comma. i.e. --mp-keyword adipo,reproductive,female --mp-search-name this argument defines that the query must be perform in the NAME field --mp-search-def this argument defines that the query must be perform in the DEFINITION field --mp-search-syno this argument defines that the query must be perform in the SYNONYM field --mp-search-opt (default: AND) defines the query statement option (AND or OR) if several keywords are defined --go-search-type type_of_input defines the type of input used to perform the query in the GO database. You can use a GO identifier (i.e. GO:0008150) or a GO term (i.e. lipid) to perform the query. To do so, you must define either 'go_id' or 'go_terms' --go-keyword keyword defines the keyword(s) (either GO id or GO term) to perform the search in the database. You can use several input keywords separating them with a comma. i.e. --go-keyword lipid,metabolism --go-search-opt (default: AND) defines the query statement option (AND or OR) if several keywords are defined --go-goa-species taxon_id Set the species for which you would like to add the GOA. You must use the taxon ID nomenclature to do so (9606: HSA, 10090: MMU or both: HSA & MMU). --synt-order NB define the synteny order (0, 1, 2 or 3) of Narcisse data --complete-with-ensembl add conservation synteny data from Ensembl to Narcisse data --omim-keyword keyword (optionnal) define the keyword to be search in the omom database. Several keywords can be added by seperating them with a comma. i.e. --omim-keyword X,Y,Z --out-result FILE (optionnal) Filename of the output results (default: OUT_result_tab.xml) re-map SNP location using locations in dbSNP. If the SNP is not in the dbSNP, the location remains the same. this argument defines that the query must be perform in the NAME field this argument defines that the query must be perform in the DEFINITION field this argument defines that the query must be perform in the SYNONYM field add conservation synteny data from Ensembl to Narcisse data display the GO ID parent (i.e. the GO id used for the request in the database to fetch the children Terms) define the species of interest by using the Taxon ID provided by NCBI. define the chromosome name define the start location of the genomic region (in bases) define the end location of the genomic region (in bases) SNP datafile to include in the annotation genomic window. File must have the following tabular format: SNP file chromosome location define the keyword to be search in the Mammalian Phenotype database (i.e. reproductive). Several keywords can be added by seperating them with a comma. defines the query statement option (AND or OR) if several keywords are defined defines the keyword(s) (either GO id or GO term) to perform the search in the database. You can use several input keywords separating them with a comma. defines the query statement option (AND or OR) if several keywords are defined Set the species for which you would like to add the GOA. define the synteny order (0, 1, 2 or 3) of Narcisse data define the keyword to be search in the omom database. Several keywords can be added by seperating them with a comma. Filename of the output results (default: OUT_result_tab.xml) Synteny conservation species. Returns metadata about the application. This includes usage information, along with any number of arbitrary application-specific metadata specified as an array of info elements, e.g. description of the various options that are passed to the application binary. Requires all the parameters with correct type, and structures representing the input files. The structure contains the name of the input file and either the contents in Base64 encoded binary form or a MIME attachment, or simply a location (URL) to the associated file. The operation returns a Job ID that can be used to retrieve job status and outputs. Same as launchJob but blocks until the remote execution is complete, and returns job outputs (as described above) as the response. This operation may only be appropriate for jobs that are not long running. Expects a Job ID to query the status of a running job. A status code, message, and URL of the working directory for the job are returned. Returns basic job statistics including start time, activation time and completion time for a given Job ID. returns the outputs from a job that is identified by a Job ID. The output consists of the urls for the standard output and error, and an array of structures representing the output files. The structure contains the name of the output file and the url from where it can be downloaded. Returns the contents of an output file as Base64 binary. The input is a data structure that contains the Job ID for a particular job, and the name of the file to be retrieved. Destroys a running job identified by a Job ID.