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.
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.