How do I predict the secondary structure from an amino acid sequence ?

The STRAP-toolbox, which is derived from the alignment program STRAP, provides several prediction methods which can be used along with Biojava. To use this toolbox it is necessary to add strap.jar to the class path.

Usage of SecondaryStructure_Predictor : An instance of SecondaryStructure_Predictor is created and the sequence set. The computation is invoked with the method SecondaryStructure_Predictor#compute() . The result is obtained with the method SecondaryStructure_Predictor#getPrediction() .

Web-Proxy: In case STRAPis unable to get into the Internet a possible reason is that a web proxy needs to be specified. This is discussed in Scripting.html.

import charite.christo.strap.extensions.*;
import charite.christo.interfaces.SecondaryStructure_Predictor;
import charite.christo.interfaces.TransmembraneHelix_Predictor;
import charite.christo.interfaces.CoiledCoil_Predictor;
import charite.christo.interfaces.PredictionFromAminoacidSequence;
import charite.christo.Web;
/*
  java   DemoPrediction
  Secondary structure elements like helices and beta sheets can be predicted from the primary structure.

  Three interfaces are derived from PredictionFromAminoacidSequence for secondary structures, coiled-coils and
  transmembrane helices.
*/
public class DemoPrediction {
    public static void main(String[] argv){
        /*INFO_PROXY*/
        /*Create an instance of SecondaryStructure_Predictor */
         PredictionFromAminoacidSequence predictor=new SecondaryStructure_Sopma();
        /* Set the sequence. */
        /* The setter allows also multiple sequences given as an array of Strings. */
        /* This improves performance for web based methods and allows some methods to compute the consensus. */
        predictor.setGappedSequences(new String[]{"MFLTRSEYDRGVNTFSPEGRLFQVEYAIEGHKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQEVYHKSTTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKDMEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHLQEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWPLPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVFGLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFLPQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNEHVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQAGQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCVDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSS"});
        /* start computation */
        predictor.compute();
        /* get the result for the first and only sequence (index 0) */
        char result[]=predictor.getPrediction()[0];
       System.out.println(new String(result));
       System.exit(0);
    }
}

License: STRAP-toolbox is distributed under the GNU-license. You should read the terms of use for the embedded tools.

Last modified: Thu Mar 5 21:15:10 Local time zone must be set--see zic manual page 2009