Calling Ebi'S Qblast In A Standalone Program
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12.9 years ago
Graslevy ▴ 240

I am currently exploring the possiblilty of developing a phylogenetic tool to support an ongoing research. Coding with Servlets, JSP and Java; To overcome the perfomance hit (in bootstrapping), I am considering using web services for sequence alignment and phylogenetic trees. My understanding is that using QBLAST does not require SOAP/REST but I want to better understand the response from QBLAST.

On the ebi website (http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_rest) the run method specifies 'sequence' as a parameter. This should be the result of the multiple sequence alignment. My concern is the format required for the clustal service. Will this maatch the response from QBLAST? Do I need to modify the alignment from blast with Jukes before sending to clustal?

Secondly, I humbly request some advise on whether to use this approach or push forward with coding Needleman-Wunsch as well as the phylograms?

Thanks!

java clustalw • 2.4k views
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12.9 years ago

What exactly should your tool do? It's hard to give any recommendations without knowing that.

Concerning QBLAST: Look at the bottom of the page (or the URL) and find the year there: 1999, which is 12 years old. In order you access the NCBI BLAST programmatically, you better have a look at:

For the phylogenetic tree, are you sure you want to build it with clustalw? It does create a tree, however, a very crude one. A better choice would be e.g. the PHYLIP package.

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Thanks for your comment, yes I noticed the qblast page. The tool is a required deliverable to satisfy the computing department. Its strange that they want an equal computing component in the project. Would you advise using the web services approach?

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btw, the research is a phylogenetic analysis of Entomophthorales...

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You didn't really say what the tool should do ;) - just find related sequences and construct a tree?

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Yes Sir. It will allow for MSA using sequences from file or BLAST search and then construct/display a phylogram. I am aware that this is unnecessary considering I can get things done elsewhere but the computing compnent is required as stated earlier.

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Then I'd go with URLAPI (remote), PHYLIP (local), and whatever feels most comfortable to stitch them together. You might also want to have a look at BioJava/Perl/Python for nice I/O handling.

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