Entering edit mode
10.9 years ago
PedroBarbosa
▴
20
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.
Maybe this will be helpful for you: "How to implement a SequenceDB by Joerg Ruedenauer "http://www.joerg-ruedenauer.de/Software/blast/blast1.html
That was exactly the implementation that i was following to perform my search but it is a old one and some classes and methods could not be used.
Anyway i started writing an implementation by my own not using biojava , instead calling the commandline blastp that i've installed in the system.
That's how we start in this field, sorry for my apparently newbie question! Thanks for the reply btw!
I may be a bit late to this thread.... I'm sure you have realised that the link supplied by seninp (although potentially usefull as a guide) is for the legacy biojava-legacy 1.8.2 API which is probably why it isn't working as you'd expect. Can you not have both packages installed on your system, and for this instance just refere to the legacy jar.? I have had a look on the bioJava site, but can't find any details of the deprecated methods / classes, and proposed ways to upgrade your old legacy stuff to the new bioJava3. However I just found this page http://biojava.org/wiki/BioJava:CookBook3:NCBIQBlastService which may have what you are looking for