Smith Waterman - Local Alignment

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BioJava contains implementation for various protein sequence and 3D structure alignment algorithms. Here is how to run a local, Smith-Waterman, alignment of two protein sequences:

public static void main(String[] args) throws Exception {

String uniprotID1 = "P69905";

String uniprotID2 = "P68871";

ProteinSequence s1 = getSequenceForId(uniprotID1);

ProteinSequence s2 = getSequenceForId(uniprotID2);

SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();

GapPenalty penalty = new SimpleGapPenalty();

int gop = 8;

int extend = 1;

penalty.setOpenPenalty(gop);

penalty.setExtensionPenalty(extend);

PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> smithWaterman =

Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.LOCAL, penalty, matrix);

SequencePair<ProteinSequence, AminoAcidCompound> pair = smithWaterman.getPair();

System.out.println(pair.toString(60));

}

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%s%s", uniProtId, seq, System.getProperty("line.separator"), seq.getOriginalHeader());

System.out.println();

return seq;

}