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BUILDING THE TAVERNA WORKFLOW 

 

 

The objective  of the exercise;

 

          -To align the DNA sequences in Fasta format from DDBJ (DNA Data Bank of Japan).

 

 

 

Building a workflow from the following diagram;

 

1. Open the DDBJ

 

2.Put DNA sequences in FASTA format in the search box  

 

3. BLAST (sequence alignment and similarity searching) 

 

4.Blast_Report  (Percent similarities and identity)  

 

 

The  modification of Taverna workflow was adapted from this figure below;

 

  

 

 

 

 

Installing the Taverna Workbench 

 

 

1. Download Taverna from http://taverna.sourceforge.net 

 

 

 

 

2.Download  a modern Java Runtime Environment (JRE) from http://java.sun.com

 

 

 

 

►  Once Taverna has loaded, you will see 3 windows:

• Advanced Model Explorer
• Workflow Diagram
• Available Services

 

  

 

 

 3. Installing Plugins

 

-Go to the ‘Tools’ menu at the top of the workbench

 

-Select the ‘Plugin manager’¨ Select find new plugins ¨

 

-Tick the boxes  for Feta and LogBook and install these plugins. Two more options ‘Discover’ and ‘LogBook’ will now have appeared at the top of the Taverna workbench alongside ‘Design’ and ‘Results’ 

 

 

 

4. Adding new services which were not designed for use in Taverna,

 

 -New services can be used in Taverna if WSDL file was supplied.

 

-Go to the DDBJ list of available web services at: http://xml.nig.ac.jp/index.html

 

 

 

 

-Click on the DDBJ blast service (http://xml.nig.ac.jp/wsdl/Blast.wsdl) and copy the web page address.

 

 

 

 

 

- Go to the ‘Available services’ panel and right-click on ‘Available Processors’ (at the top of the list).

- Select ‘Add new WSDL scavenger’.

 

 

 

 

 

 

 

- Enter the Blast Web service address.

 

  

 

 

- Scroll down to the bottom of the ‘Available Services’ panel and look at the new DDBJ service that is now included. 

 

  

 

 

5.  Adding Processor INPUT 

 

5.1 Import the ‘searchSimple’ service from the DDBJ service into a n ew workflow model. SearchSimple is a processor used to execute nucleotide BLAST for DNA query vs. DNA database. 

 

 

 -Right-click on ‘searchSimple’ and import it into the workbench by selecting ‘Add to Model’ 

 

 

  

 

 

 -Go to the AME and expand the [+] next to the newly imported ‘simpleSearch’ service. You will see: ¤ 3 input (Green arrow pointing up) and 2 output (purple arrow pointing down)  

 

  6. Adding Workflow Input

 

 

 -Right-clicking on ‘Workflow Input’ and selecting  ‘create new Input’ . 

 

 

 

 

-Type a name ‘Fasta sequence’

 

 

 

Click ‘OK’.

 

 

 

- For the other two workflow inputs ‘Database’ and ‘Program’  Do the same steps  as ‘FASTA_Sequence’.

We will get,

 

 

-Connect the input  ‘FASTA_Sequence’  to the ‘searchSimple’ service by right-clicking on ‘FASTA_Sequence’  and connecting  to ‘search Simple’ by choosing an Input as query.

 

 

 

 

 

 

-Connect the input  ‘Database’  to the ‘searchSimple’ service by right-clicking on ‘ ‘Database’  and connecting  to ‘search Simple’  by choosing an Input as database.

 

 

 

 

 

 

 

 

 -Connect the input  ‘Program’  to the ‘searchSimple’ service by right-clicking on ‘‘Program’  and connecting  to ‘search Simple’  by choosing an Input as program.

 

 

  

 

 

7. Create  a Workflow output.

 

-Click on the Workflow output. Create New Output  as  ‘blast_report’. 

 

  

 

 

-Click right at ‘blast_report ‘ and connect to search ‘search Simple’.

 

 

 

 

 

 

 

8. Run the workflow by selecting ‘run workflow’ from the ‘File’ menu at the  top of the workbench.

 

 

 

 

 

 9. To align the DNA sequences in Fasta format of an unknown Bacteria species, Ehrlichia  sp. with the Database DDBJ (DNA Data Bank of Japan). The DNA sequence of 16S rRNA gene of  Ehrlichia sp. HF565 was retrieved via Acceesion Number AB275138.

 

9.1 Dowdload Fasta format of Ehrlichia sp. HF565 via accession number AB275138.

 

 - Sequence Fasta format.

>AB275138|Ehrlichia sp. HF565 gene for 16S rRNA, partial sequence, isolate:
tacggtccagactcctacgggaggcagcagtggggaatattggacaatgggcgaaagcct
gatccagctatgccgcgtgagtgaagaaggccttcgggttgtaaagctctttcaataggg
aagataatgacggtacctatagaagaagtcccggcaaactccgtgccagcagccgcggta
atacggagggggcaagcgttgttcggaattattgggcgtaaagggcacgtaggtggacta
gtaagttaaaagtgaaataccaaagcttaactttggagcggcttttaatactgctagact
agaggtcgaaagaggatagcggaattcctagtgtagaggtgaaattcgtagatattagga
ggaacaccagtggcgaaagcggctatctggttcgatactgacactgaggtgcgaaagcgt
ggggagcaaacaggattagataccctggtagtccacgctgtaaacgatgagtgctaaatg
tgaggattttatctttgtattgtagctaacgcgttaagcactccgcctggggactacggt
cgcaagactaaaactcaaaggaattgacggggacccgcacaagcggtggagcatgtggtt
taattcgatgcaacgcgaaaaaccttaccactttttgacatgaaggtcgtatccccctaa
cagggggagtcagtccggctggaccttacacaggtgctgcatggctgtcgtcagctcgtg
tcgtgagatgttgggttaagtcccgcaacgagcgcaaccctcatccttagttaccaacag
gtaatgctgggcactctaaggaaactgccagtgataaactggaggaaggtggggatgatg
tcaagtcagcacggcccttataagg

 

 9.2 Input fasta sequenece of Ehrlichia sp. HF565  by clicking  New Input  ‘then copy the fasta sequence in to the blank.

 

 

 9.3 Input the ‘Database’ as ‘ddbjbct’  by clicking New Input then type ‘ddbjbct’ .

 

(ddbjbct – DDBJ Bacteria division is reference sequence database for FASTA).

 

9.4 Input the ‘Program as ‘blastn’ by clicking New Input then type ‘blastn’ .

 

 

 

9.5  Click on Run work flow

 

9.6 Result of BLAST (blast_report)

 

 

9.7  Save  the RESULT as ‘blast-report Ehrlichia Hf5652.xml’.