What can help me out in understanding the actual concept of a BLAST. I have to write a Blast. This is my Semester Project. This is a challenge for me.
Please define "I have to write a Blast."
It means I have to write a blast tool for bioinformatics department of our campus and I don't get any source that where I can start.
Download BLAST. Why reinvent the wheel?
I think Brian Bushnell knows many things in java programming
BB's major works use bash. The guy that uses Java for virtually everything is Pierre. I mean, he creates Bio Java solutions named for BioStar threads! (Examples: https://github.com/lindenb/jvarkit/wiki/Biostar78400, https://github.com/lindenb/jvarkit/wiki/Biostar78285, https://github.com/lindenb/jvarkit/wiki/Biostar77288)
Please tell something about project relate. I mean that help me in sorting out blast algorithm.
OK, why do you want to use BioJava?
Because I have to write this software in java language and that is why I think that I have to use the BioJava libraries.
My feeling: you currently have no idea of what you're doing. Go back to your principal investigator and ask for more information.
What would you say that I have to use...because I'm totally at the beginning stage.
Use BLAST. Change your project.
The shell scripts are just wrappers; the actual programs are in Java :) But, I have not used BioJava.
Check "The Statistics of Local Pairwise Sequence Alignment" webinar given by no other than Altschul himself.
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