Question: Biojava secondary structure prediction
0
gravatar for ewa_kania-15
5.9 years ago by
United Kingdom
ewa_kania-150 wrote:

Is there any method to use in biojava to predict secondary structure from a given sequence?

Or if not does any anyone how can i implement it? any source code? Any exe to recommend?

ADD COMMENTlink modified 5.9 years ago by sbliven30 • written 5.9 years ago by ewa_kania-150
1
gravatar for sbliven
5.9 years ago by
sbliven30
Switzerland/Villigen/Paul Scherrer Institute
sbliven30 wrote:

There's a DSSP implementation in the structure module, called SecStruc. I recommend using the latest BioJava snapshot from github for this code, as there have been some recent bug fixes.

import org.biojava.bio.structure.secstruc.SecStruc;
import org.biojava3.structure.StructureIO;
import org.biojava.bio.structure.Structure;
...
Structure s = StructureIO.getStructure("1BSP");
SecStruc sec = new SecStruc();
sec.assign(s);
for(Group g : sec.getGroups()) {
     SecStrucState state = (SecStrucState) g.getProperty("secstruc");
     if(state != null) System.out.print(state.getSecStruc().type);
}
System.out.println();

The code is very rough and should be considered 'beta'. There may be a few minor differences to the official DSSP implementation.

ADD COMMENTlink written 5.9 years ago by sbliven30

In case anyone stumbles across this post, biojava 4.2 officially includes secondary structure prediction and is tested for DSSP compatibility.

ADD REPLYlink written 3.9 years ago by sbliven30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1500 users visited in the last hour