Greetings all,

This is kind of off the topic , but since I am from a computer science background and I have very little knowledge in bioinformatics ,i thought I can get some help form here. In the project I am working with, I have to find the 'epitope' sequence in a PDB file.At the moment they have implemented some logic (not very good, as they say) for it using Perl ,but for the requirements they ask I need to do it in Java.
And also there is a requirement to highlight CRD3 region in JMol.
Any tips where I found start?

Thanks in advance.
umanga
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