Extract_unique_proteins_from_blast_resultsblastFile00 inputs the xml format of the blast results 2010-03-19 03:21:20.950 GMT C:\Users\You\Documents\my_blast_results.tab 2011-03-24 15:21:18.503 GMT The URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not a file location). 2011-03-24 15:20:55.164 GMT The URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not 2011-03-24 15:20:42.61 GMT The URL or file path location of the tab-delimited format of the Blast results. 2011-03-24 15:20:06.729 GMT C:\Users\You 2011-03-24 15:20:32.41 GMT tfasta00 fasta file of the target proteins to extract the sequences 2010-03-19 03:19:27.444 GMT File 2011-03-24 15:21:59.270 GMT Fasta file of the target proteins to extract the sequences. Add as file location. 2011-03-24 15:21:53.195 GMT Fasta file of the target proteins to extract the sequences. 2011-03-24 15:21:32.450 GMT File : C:\Users\You\Documents\target_fasta.faa 2011-03-24 15:22:34.14 GMT unique_identifiers Unique identifiers that appear in the FASTA file but not in the BLAST file. Identifiers are separated by new lines. 2011-03-24 15:28:07.208 GMT gi|321313668|ref|YP_004205955.1| gi|321312432|ref|YP_004204719.1| gi|321314996|ref|YP_004207283.1| 2011-03-24 15:28:18.998 GMT blasted_identifiers gi|321313668|ref|YP_004205955.1| gi|321312432|ref|YP_004204719.1| gi|321314996|ref|YP_004207283.1| 2011-03-24 15:27:27.684 GMT Identifiers of the target genome from the BLAST results. These identifiers are those that are similar to the source proteome. 2011-03-24 15:26:18.245 GMT Read_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_unique_proteinsxml_result0gi_lines_val00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true xml_result 0 text/plain 0 gi_lines_val 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTfasta_parsergi_val0tfasta_in0cfasta_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true gi_val 0 text/plain java.lang.String true tfasta_in 0 text/plain 0 cfasta_out 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlblastFileExtract_unique_proteinsxml_resultRead_Text_FilefilecontentsTfasta_parsergi_valExtract_unique_proteinsgi_lines_valTfasta_parsertfasta_intfastaunique_identifiersTfasta_parsercfasta_outblasted_identifiersExtract_unique_proteinsgi_lines_val The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created. 2010-03-19 03:23:47.653 GMT 7045bed3-10bd-4d68-9c66-0135b0ed2dde 2011-03-24 15:28:27.232 GMT Extract unique proteins from blast results 2010-03-19 03:16:29.89 GMT fetchEnsemblSeqsAndBlast 2010-03-15 11:30:59.109 GMT 2010-03-19 03:14:00.733 GMT b2579890-b32e-4be4-975b-28659feea68f 2011-03-24 13:12:29.54 GMT Bela Tiwari 2010-03-15 11:30:59.109 GMT 782c8659-5afb-4518-a8c3-0376a0884816 2011-03-24 13:52:32.878 GMT 4d837fd7-5124-4e7c-964b-17de794236cc 2011-03-24 15:25:33.719 GMT nclteamc 2010-03-19 03:15:57.858 GMT Workflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome 2010-03-19 03:18:26.823 GMT This 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 will overwrite files you have previously created. All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use. 2010-03-15 11:30:59.109 GMT