Liliopsida Protein Alignment
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This workflow retrieves Liliopsida chloroplast petb gene sequences from NCBI Nucleotide, removes duplicate sequences and saves the results at BioExtract Server. These results are then converted into GenBank format and fed into Fetch Translation, which removes the translation from the CDS coding region. Translations are then used to build a multiple alignment using ClustalW.
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1. Lushbough CM, Bergman M.K, Lawrence C J, Jennewein D, Brendel V, BioExtract Server - An Integrated Workflow-Enabling System to Access and Analyze Heterogeneous, Distributed Biomolecular Data, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11 September 2008, http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.98, Accessed at: 28 October 2008
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Great!
Maybe you can add a check for the md5 of the sequences, to be sure they have been downloaded properly (in case you have problems with internet connection).
Moreover, I think it would be important for the workflow to write down somewhere the version of the ncbi database when the sequences are downloaded, so it would be easier to reproduce its results.
Also the parameters of clustalw and its version are important.
Have you tried this workflow with some data? Can you provide an example of how to use it?
Giovanni Dall'Olio, thank you for your kind comments. We just recently discovered myExperiment and are very excited about it. This site has motivated us to begin working on functionality to import and export our workflows as XML. Hopefully, we can use scufl so that in some cases we can share with Taverna.
For now, if you would like a copy of this workflow,
1) log into bioextract.org as a registered user
2) click the workflow tab
3) execute the workflow
4) click the "Current Workflow" node on right (above the workflow tree)
5) provide a name and description and click save.
Now you have your own copy of the workflow. You can expand the workflow, click the query node and change the query values. You can click the tool nodes and change the parameter settings.
You are correct, documenting the NCBI version number would be very important. Another way one could reproduce workflow results would be to save the dataset and then run the workflow starting with the saved data rather than going back to NCBI.
BioExtract Server workflows can now be imported into your workspace at bioextract.org. To Import this workflow, sign into the system as a registered user then click the "Create and Import Workflows" node in the Workflows tree on the Workflows tab. Once you've uploaded the workflow, you can modify it to meet your needs (e.g. change tool parameters or queries) my expanding the workflow in the tree.