Command-line input for 'short queries' in blastp using Geneious
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4.2 years ago

I am trying to search some short sequences using Geneious blastp search with the standard parameters.

The problem is that Geneious does not automatically detect for small sequences (the BLAST website does!). Therefore, I am looking for the equivalent of the blastp parameter short queries (automatically adjust parameters for short input sequences). Does this exist as a command line argument? Alternatively, but even more conveniently, does Geneious have this parameter hidden away somewhere in its interface?

Edit: I found this Link on the Geneious website (unfortunately focused on blastn). It mentions the weakness of Blast when it comes to short sequences; however, as the option in blastp for short queries exists, I still hope that there is a viable solution.

command line blastp geneious ncbi short queries • 1.0k views
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Maybe you could use -task blastp-short as mentioned in this post - Blast Settings For Short Sequences

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Thanks! -task blastp-short would work I guess. However, I just realized that Geneious does not seem to offer an easy option how to include this parameter. Have you worked with this software before and know how I could include this argument?

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Geneious is a commercial tool and I have never used it, you may not find many people on this forum who may have used it.

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You should ask geneious tech support. It is likely that the option is not implemented in geneious GUI for blastp.