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BioMoby web services

Available BioMoby web services ordered by MobyCentral and authorities

To test the following services use the simple client of the moby dashboard:
http://www.biomoby.org/

Endpoint: http://moby.ucalgary.ca/moby/MOBY-Central.pl Namespace (URI): http://moby.ucalgary.ca/MOBY/Central
mips.gsf.de
getAllGeneticElements	Retrieves all genetic element names matching given search string (for example all AGI locus codes for search string "At").
getClonesByFreeText	Retrieves all clone annotation for given search text.
getClonesByName	Retrieves annotation for given clone name.
getContigsByFreeText	Parses Element Names out of any text-xml or text-formatted (output sorted by alphabet).
getContigsByName	Retrieves Contigs list for a contig name.
getElement	Get genetic element report from MIPS PlantsDB.
getElementAnnotation	Retrieve annotation for the given genetic element.
getElementsByFreeText	Retrieves a list of basic genetic elements with names matching the input string.
getElementsByName	Retrieves a basic genetic element by its exact name.
getElementsForContig	Retrieve all genetic elements for given contig as collection of plain-text objects (eg. mth2-11e1).
getElementsOfType	Retrieves a list of all genetic elements of a given element type.
getGeneticElementNameByFreeText	Retrieves genetic element names related to the given keyword from all MIPS databases (arabidopsis, medicago, maize, rice).
getGeneticElementsOfType	Retrieve all genetic elements for given element type.
getProteinSequence	Retrieves Protein sequence for a genetic element name.
getSplicedSequence	Retrieves Spliced sequence for a genetic element name.
getUnsplicedSequence	Retrieves Unspliced sequence for a genetic element name.

mpiz-koeln.mpg.de
Blast_Against_RefSeq_Complete _Sequenced_Organisms	Runs a blastp search against the RefSeq database, which includes only complete sequenced organisms.
buildMultipleAlignmentWithMAFFT	Builds a multiple alignment with MAFFT from a set of fasta files.
BuildPhylogeneticTreeFromFasta Alignment	Builds the most accurate phylogenetic tree. For small trees (< 20 sequences) a maximum likelihood approach (Phyml) and for greater trees a very good and high performance neighbor joining algorithm (BioNJ) is used.
get_agi_code_by_keyword	Gets a keyword as input, runs a fulltext search in the alternative names and the description lines of the AFAWE database and returns a collection of AGI locus codes with description.
get_go_information_by_go_term	Returns for a given GO term name, description and GO process (molecular function, biological process, cellular component).
get_GO_Term_by_Database_ID	Returns for a given RefSeq ID GO terms from different databases (GO annotation files were downloaded from Gene Ontology).
get_other_database_accessions _by_database_accession	Gets a database identifier as input and returns all stored alternative names (database identifiers, accessions, locus codes, ...) from the AFAWE database.
getAutomaticAndManualAnnotation ByAFAWE_ID	Returns available manual annotations (manual annotation added by users) and automatic annotations (predicted by Sifter) for a given AFAWE ID (http://bioinfo.mpiz-koeln.mpg.de/afawe/).
GetConservedDomainsFromFasta Alignment	Extracts conserved regions from fasta alignment.
GetInAndOrthologsFromRefSeq	Runs a iterative Blastp searches against the RefSeq database with only full sequenced organisms. Inparalogs and Orthologs are returned in fasta format.
RPSBlast	Runs a RPSBlast search against the Conserved Domain Database of the NCBI. Result is the raw blast result.

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BioMoby web services