Baywatch Solutions2011-11-22T12:35:12+00:00/groups/2462013-05-08T14:52:01+00:00Andrew David King shared Test for OrthologuesWarning: The files are hardcoded in to the beanshell of this workflow. Given an orthlog file for an organism from http://www.ebi.ac.uk/integr8/FtpSearch.do ? orgProteomeId=22602, find proteins that are orthologous to proteins in another oragnsims, e.g., B.subtils. Outputs percent.urn:uuid:0602109f-5569-468c-b6cf-db3ee82c367bAndrew David King2013-05-08T14:52:01+00:00Fergus shared KEGG pathway analysisThe KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi_manual.html#label :42. A list of KEGG Ids in a tabular format is produced, the first element contains the input ID, the second element is the KEGG ID and the third element is a string confirming the corresponding existence of the proteins in both databases used. This tabular format is then split into three segment …urn:uuid:c5678287-a58f-4796-b537-7ec18e25ab9aFergus2013-05-08T14:52:01+00:00Andrew David King shared Fetch EMBL FileFetches an EMBL file using the EMBL id. Creates file to a specified location.urn:uuid:be36422c-b4b2-410e-b20c-6892f682af9eAndrew David King2013-05-08T14:52:01+00:00Andrew David King shared Fetch Fasta and Genbank filesFetches fasta and genbank files for a given identifier., e.g., CP000256urn:uuid:64bd5cb0-9253-48b2-a0b4-11605bbaf22fAndrew David King2013-05-08T14:52:01+00:00Andrew David King shared KEGG Pathway AnalysisThe KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi_manual.html#label :42. A list of KEGG Ids in a tabular format is produced, the first element contains the input ID, the second element is the KEGG ID and the third element is a string confirming the corresponding existence of the proteins in both databases used. This tabular format is then split into three segment …urn:uuid:6c18ebd4-d92d-47cf-9775-099b7d098718Andrew David King2013-05-08T14:52:00+00:00Andrew David King shared BlastandParse1This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you …urn:uuid:e1dc8654-596e-4f35-9307-bb8f0a724598Andrew David King2013-05-08T14:52:00+00:00Andrew David King shared BlastandParse2This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you …urn:uuid:22f10474-eb50-4e7d-ad45-e9956b33d11eAndrew David King2010-03-11T13:56:11+00:00Akshayshah88 joined the Baywatch Solutions groupurn:uuid:51f4e300-dbad-4f3c-ab2f-57d32e745780Akshayshah882010-03-11T12:12:56+00:00Haakon berven joined the Baywatch Solutions groupurn:uuid:64cccdf1-e0a6-4d94-995c-a1c47f8f23d3Haakon berven2010-03-11T11:22:25+00:00Fergus joined the Baywatch Solutions groupurn:uuid:64fb0ebd-abbf-4bfe-9e3a-9cf2a9c3af24Fergus2010-03-11T08:41:09+00:00Monica Bhaskar joined the Baywatch Solutions groupurn:uuid:11eec3a7-87cc-480d-a678-16dc31a41658Monica Bhaskar2010-03-10T19:18:37+00:00Peter Hebden joined the Baywatch Solutions groupurn:uuid:085eac68-d30c-4814-8ef3-1e03fc16a3dfPeter Hebden