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  • Pedro_Barbosa
    Junior Member
    • Mar 2012
    • 1
    #1

    Standalone Blast using Biojava

    I'm trying to run blastp using some biojava packages.

    I realized a class that can perform BLAST searches should be implementing the Interface SeqSimilaritySearcher from the package org.biojava.bio.search.


    Unfortunately, i need to give a SequenceDB to this method. I want to do the search on protein files in FASTA format, like the nr. How to get a SequenceDB for that?

    I read somewhere that a package called org.biojava.bio.program.indexdb could solve the problem but i cant figure out how.
    Tags: biojava, blastp, database, java
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