Re: [Seqan-dev] SeqAn for proteomics searches in KNIME?

[Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>]

Am Dienstag, 20. November 2018, 21:59:45 CET schrieb Lee S Parsons:
> Hello
> 
> I would like to use SeqAn to align peptide sequences to protein (FASTA)
> databases.  Is there a way to do this?
> 
> I work with a lot of proteomics data in KNIME, and the OpenMS group
> suggested I look into SeqAn for what I'm trying to do next.  While you
> probably know that the OpenMS project already has several spectral
> matching search algorithms built in to it, the project only has one de
> novo algorithm (compnovo).  While compnovo is a great tool, by virtue of
> being a de novo algorithm it does not do sequence alignment.  I can
> easily get a list of peptides from compnovo, and I can use the Vernalis
> tool set to read in a FASTA database, but I don't know of a good tool to
> score the sequence similarities. 
> 
> Can SeqAn do this?  I have had a hard time with the documentation
> (particularly in KNIME) and I haven't been able to find any workflows
> that show anything quite like this with SeqAn in KNIME.
> 
> thank you!
> Lee


Dear Lee,

are you looking for a stand-alone tool? Have you tried Lambda, our protein 
alignment program?
https://github.com/seqan/lambda

I am afraid there is no KNIME integration, yet, but it would not be difficult 
to add.

Best regards,
Hannes
-- 
Hannes Hauswedell

Scientific staff & PhD candidate
Freie Universität Berlin / Max Planck Institute for Molecular Genetics

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