NCBI BLAST+ in KNIME?

KNIME Analytics Platform
1

Is there any plan to make the NCBI BLAST+ suite available as KNIME nodes?  These could be useful for both the NGS and OpenMS communities (amongst others).  Making the commands "makeblastdb", "blastx", "blastp", and "blastn" into nodes would be very useful; adding in "tblastx", "tblastn", and "blastdbcmd" would be great as well. 

The download info is all here if someone wants to take a look at it:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Thank you

2

While BLAST+ does not seem to be available currently as a node, an OpenMS developer suggested SeqAn as a way to try to accomplish the same goal.  SeqAn is available as a node in trusted community for KNIME 3.1, though not currently for KNIME 3.5. 

3

Hi @lparsons42,

first of all, thank you for bringing this topic up and sorry for quite a delay with response. Good news is that we are currently working on wrapped metanodes which will allow to query NCBI BLAST and some other services. Once we have it ready we are going to write a blog post with an example workflow illustrating their usage, which will be published at some point in the future. So please stay tuned :wink:

Best regards,
Oleg

4

@oyasnev

Is there any update on the BLAST metanode? I recently reached out to the SeqAn group and found that - at least at this time - SeqAn is not ready to do database searches (or at least, not for protein databases). If there is any news on this I would love to hear it.

thank you!
Lee

5

Hi @lparsons -

Here is the blog post that Oleg was referring to - it was just published a couple of weeks back and contains a workflow. Maybe it will help?

https://www.knime.com/blog/blast-from-the-past

7

Thank you for pointing that out @ScottF! It is certainly useful, though there are a couple things that impede this being as useful as a locally-executable BLAST node for KNIME:

  1. There is no easy way to specify a custom db for this. There is likely some syntax magic that would allow me to specify a given species in this, but if I need a combination or subset of species that would be much more difficult.

  2. NCBI traditionally throttles bandwidth to users who submit many jobs in a short amount of time. One of my interests here is in taking the output of the OpenMS “compnovo” wrapper and running them through BLAST, however this can easily lead to hundreds if not thousands of peptide sequences.

This is certainly helpful regardless! I have managed to get at least a few peptides going through already. Thank you!