/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.alignment;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
import org.biojava.nbio.core.util.ConcurrencyTools;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
public class CookbookMSA {
public static void main(String[] args) {
String[] ids = new String[] {"Q21691", "Q21495", "O48771"};
try {
multipleSequenceAlignment(ids);
} catch (Exception e){
e.printStackTrace();
}
}
private static void multipleSequenceAlignment(String[] ids) throws Exception {
List<ProteinSequence> lst = new ArrayList<ProteinSequence>();
for (String id : ids) {
lst.add(getSequenceForId(id));
}
Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(lst);
System.out.printf("Clustalw:%n%s%n", profile);
ConcurrencyTools.shutdown();
}
private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {
URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));
ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);
System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());
return seq;
}
}