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

[Lee S Parsons <pars0080@umn.edu>]

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

-- 
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Lee S Parsons, PhD
RIS Biological Mass Spectrometry Analyst | Minnesota Supercomputing Institute | www.msi.umn.edu
University of Minnesta | umn.edu
lparsons@umn.edu | 612-624-4466