Is there any BLAST node for KNIME that is only based on the publically available algorithm - not based on commercial solutions?
It looks as if there may be a node of interest for you from the ETH, check here: http://hcdc.ethz.ch/index.php?view=article&id=25 and let us know if this is what you were looking for.
Thanks for your answer.
Yes, I know this site (http://hcdc.ethz.ch/downloads/hcbi/update-site-release/), but it seems that it is not working anymore correctly.
The functionality of this node is: "This node provides the BLAST search for a nucleotide sequence against the NCBI nucleotide database (blastn)."
But I am searching for a node that uses the publically avaiblable BLAST executable - also able to search in local DBs.
Oops, my apologies for suggesting such a goose chase.
I believe what you want to do is possible through the External Tool Node (ETN) in combination with the blast+ executables, but it won't be the easiest thing in the world to set up.
In broad strokes, you would want to call a shell script from an ETN using a table with a single cell of sequence data as your input. In this script, you will call blast with your sequence file, database, and output filename as arguments. Finally, the need for a shell script comes into play as you will then need to reread, reformat and rewrite the blastn output file in a way that plays nicely with KNIME. For example, I would try to craft the blast output into a csv file with a one line header.
I plan to setup a demo of this process but at the moment we are quite busy with the KNIME Desktop 2.6 release and we don't have enough spare cycles to generate a working example. Once we get 2.6 pushed out (end of July) I will come back to this and put together something nicer.
Both the executables and the databases for blast are located here:
Finally, as a nod to one of our development partners and for the general interest of anyone else reading this thread in the future, I'd like to mention the Korilog Bioinformatics Extensions for KNIME would also probably get the job done and with much less hassle (but it obviously doesn't satisfy your specific requirements of being noncomercial).
Yes, it would be nice to see an example workflow with the External Tool Node (ETN). We use a similar approach to call executables - with an own C-Shell (csh) node that executes a csh command. This csh node is based on the bash node in the NGS extensions.
But this csh node is only used as a work-around because one has to reread the generated output files and because such workflows are not easily transferable.
So if anybody can offer a solution to encapsulate a BLAST algorithmn in the KNIME node, this is highly appreciated.