BioJava:CookBook3:HmmerService

From BioJava

A simple demo that fetches a protein sequence from the UniProt web site, submits it to the Hmmer3 service and prints the results.

/* 
 * @since 3.0.3
 */
	public static void main(String[] args){
 
		try {
			// first we get a UniProt sequence
			String uniProtID = "P26663";
			ProteinSequence seq = getUniprot(uniProtID);
 
 
			// now we submit this sequence to the Hmmer web site
			HmmerScan hmmer = new RemoteHmmerScan();
 
			SortedSet<HmmerResult> results = hmmer.scan(seq);
 
 
 
			// let's print the obtained annotations
 
			System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
					"Domain","ACC", "Start","End","eValue","Description"));
 
			int counter = 0;
			for (HmmerResult hmmerResult : results) {
				//System.out.println(hmmerResult);
 
				for ( HmmerDomain domain : hmmerResult.getDomains()) {
					counter++;
					System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",
							counter,
							hmmerResult.getName(), domain.getHmmAcc(), 
							domain.getSqFrom(),domain.getSqTo(),
							hmmerResult.getEvalue(), hmmerResult.getDesc()
							));
 
				}
 
			}
 
		} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}
 
	/** Fetch a protein sequence from the UniProt web site
	 * 
	 * @param uniProtID
	 * @return a Protein Sequence
	 * @throws Exception
	 */
	private static ProteinSequence getUniprot(String uniProtID) throws Exception {
 
		AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
		UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
 
		ProteinSequence seq = new ProteinSequence(uniprotSequence);
 
		return seq;
	}

This will create this output:

#	         Domain	       ACC	Start	End	  eValue	Description
1	     HCV_capsid	PF01543.11	    2	  115	0.00e+00	Hepatitis C virus capsid protein
2	       HCV_core	PF01542.12	  116	  190	1.09e-43	Hepatitis C virus core protein
3	        HCV_env	PF01539.11	  193	  382	0.00e+00	Hepatitis C virus envelope glycoprotein E1
4	        HCV_NS1	PF01560.11	  386	  729	0.00e+00	Hepatitis C virus non-structural protein E2/NS1
5	        HCV_NS2	 PF01538.1	  811	 1005	0.00e+00	Hepatitis C virus non-structural protein NS2
6	  Peptidase_S29	 PF02907.9	 1056	 1203	0.00e+00	Hepatitis C virus NS3 protease
7	     Flavi_DEAD	 PF07652.8	 1294	 1355	8.20e-06	Flavivirus DEAD domain
8	       HCV_NS4a	PF01006.14	 1658	 1711	7.20e-25	Hepatitis C virus non-structural protein NS4a
9	       HCV_NS4b	PF01001.13	 1728	 1921	0.00e+00	Hepatitis C virus non-structural protein NS4b
10	       HCV_NS5a	PF01506.13	 1974	 1996	2.10e-10	Hepatitis C virus non-structural 5a protein membrane anchor
11	    HCV_NS5a_1a	 PF08300.7	 2006	 2067	1.40e-34	Hepatitis C virus non-structural 5a zinc finger domain
12	    HCV_NS5a_1b	 PF08301.7	 2068	 2168	2.80e-45	Hepatitis C virus non-structural 5a domain 1b
13	     HCV_NS5a_C	 PF12941.1	 2179	 2419	0.00e+00	HCV NS5a protein C-terminal region
14	         RdRP_3	PF00998.17	 2422	 2932	0.00e+00	Viral RNA dependent RNA polymerase