searching for homology in protein db

Question

[alsu.wh]

Hello All,

I am a computer science student and new in biology world. I am trying to use BioJava classes to search in downloaded proteins database for homology. After entering a protein sequence, the result should be list of species that have the same protein sequence homology. My questions are:

• Is what I am trying to do possible?
• Which data set do I need to download and which website is better?
• Which BioJava class/es should I use?

Thanks

[Ram]

Risking an off topic comment, why not simply use NCBI's BLAST? It is a well tested popular software that can be tailored to do the exact same thing you're trying to do with your custom software. Why reinvent the wheel?

Answer 1

[Prakki Rama]

Not related to BioJava, but check if this biostar post will help you.