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I would like to blast a peptide sequence against all available plant proteome databases, i.e. a blastp metaproteome analysis.

What tools are available? Which database can I use?

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  • $\begingroup$ Welcome to the site lars. You seem aware of blastp, did it not solve your problem? Or do you expect something else of blastp? Could you explain what have you tried? (to avoid suggesting the same you have already done) $\endgroup$
    – llrs
    Oct 28 '18 at 10:09
  • $\begingroup$ Thank you for the very quick reply. So far I installed ncbi-blast-2.7.1+. With makeblastdb I generated *.phr, *.pin, *psq from a fasta. I now try blastp against this database. Next steps would be to compile a metadatabase from all plant proteome databases I can find. I wonder if all of this work has already been done. Is there a website/API that I can use? I simply want to find all plant proteins which contain the amino acid sequence TEKKRRETVEREKE. Thanks. $\endgroup$
    – lars20070
    Oct 28 '18 at 10:48
  • $\begingroup$ Please edit the question to include this information. In addition, what sequences are in your fasta file? I think that you can download fasta files from NCBI. You could download the sequences from plants proteins and make the database from that (if this is not already what you did) $\endgroup$
    – llrs
    Oct 29 '18 at 8:03
  • $\begingroup$ At the moment, I work only with arabidopsis thaliana. Is there a plant meta-database? My main objective is to figure out in which plant species this peptide is expressed. $\endgroup$
    – lars20070
    Oct 29 '18 at 8:25
  • $\begingroup$ For example, PPDB is only for arabidopsis thaliana and maize. $\endgroup$
    – lars20070
    Oct 29 '18 at 8:40
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A simple BLAST on the UniProt website does the trick (target database plants).

Best matches are subsequences ETVEREKE and EKKRRETV in Green alga and Eelgrass respectively.

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