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r7 - 18 Oct 2004 - 10:12:00 - StefanEgglestoneYou are here: myGrid wiki >  Main Web  > StefanEgglestone > BioinfWorkflows
Workflow texts are attached to this page. The following table gives example inputs

Name Author Description Example input Version of Taverna required

SRSQueryUsingUSAAndFormat Stefan Rennick Egglestone Looks up sequence specified by SRS USA, then converts sequence to specified format

USAembl-acc:AL526645
formatembl
Any (tested on 0.1beta6 and upwards)

SRSQueryToBlastNCBI Stefan Rennick Egglestone Looks up sequence specified by SRS USA, and uses blastn at NCBI to return similar sequences embl-acc:AL526645 Any (tested on 0.1beta6 and upwards)

ClustalwLocalConcat Stefan Rennick Egglestone Looks up two sequences specified by USAs, and then uses clustalw web service at the DDBJ to align them against each other.
id1embl-acc:AF089088
id2embl-acc:AF089091
Tested on 0.1beta10, but probably works on all earlier versions

AccNumListToClustalw Stefan Rennick Egglestone Given a list of SRS USAs, uses clustalw at DDBJ to align the nucleotide sequences for each USA against each other List of USAs eg AF089088,AF089091 CVS head (or any releases after 0.1beta10)

ProteinNameToCrossReferencedAccessionNumbers Dr Peter Li Given a name of a protein, searches the description line of all records in SwissProt to find records containing that name. For each found, looks up any embl accession numbers referenced in the record. SWISSPROT-des:apolipoprotein Probably any

workflowacombined.xml Processors added by me to Hannah's original workflow Run this workflow and then use the "save as website" option the results panel and you'll get hyperlinked files saved out representing Hannah's results load from workflowainput.xml below probably need CVS head (I don't think that 0.1beta11 has the required functionality)

workflowacombinedv2.xml Processors added by me to Hannah's original workflow Same as workflowacombined.xml, but adds links to Entrez at NCBI to the html output load from workflowainput.xml below probably need CVS head (I don't think that 0.1beta11 has the required functionality)

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Topic attachments
I Attachment Action Size Date Who Comment
elseEXT ClustalwLocalConcat manage 2.5 K 24 Jul 2006 - 09:39 StefanEgglestone  
xmlxml workflowacombinedv2.xml manage 17.0 K 24 Jul 2006 - 09:39 StefanEgglestone  
elseEXT SRSQueryToBlastnNCBI manage 2.4 K 24 Jul 2006 - 09:39 StefanEgglestone  
xmlxml workflowainput.xml manage 3.6 K 24 Jul 2006 - 09:39 StefanEgglestone  
elseEXT ProteinNameToCrossReferencedAccessionNumbers manage 1.5 K 24 Jul 2006 - 09:39 StefanEgglestone  
elseEXT AccNumListToClustalw manage 1.9 K 24 Jul 2006 - 09:39 StefanEgglestone  
xmlxml workflowacombined.xml manage 16.4 K 24 Jul 2006 - 09:39 StefanEgglestone  
elseEXT SrsQueryUsingUSAandFormat manage 1.5 K 24 Jul 2006 - 09:39 StefanEgglestone  
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