<h2 id="calculating-a-local-alignment">Calculating a local alignment</h2>

<java> public static void main(String[] args){

`       String targetSeq = "CACGTTTCTTGTGGCAGCTTAAGTTTGAATGTCATTTCTTCAATGGGACGGA"+`

`                 "GCGGGTGCGGTTGCTGGAAAGATGCATCTATAACCAAGAGGAGTCCGTGCGCTTCGACAGC"+`

`             "GACGTGGGGGAGTACCGGGCGGTGACGGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACA"+`

`             "GCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGCGGTGGACACCTACTGCAGACACAACTA"+ `

`             "CGGGGTTGGTGAGAGCTTCACAGTGCAGCGGCGAG";`

`       DNASequence target = new DNASequence(targetSeq,`

`               AmbiguityDNACompoundSet.getDNACompoundSet());`

`       `

`       String querySeq = "ACGAGTGCGTGTTTTCCCGCCTGGTCCCCAGGCCCCCTTTCCGTCCTCAGGAA"+`

`             "GACAGAGGAGGAGCCCCTCGGGCTGCAGGTGGTGGGCGTTGCGGCGGCGGCCGGTTAAGGT"+`

`             "TCCCAGTGCCCGCACCCGGCCCACGGGAGCCCCGGACTGGCGGCGTCACTGTCAGTGTCTT"+`

`             "CTCAGGAGGCCGCCTGTGTGACTGGATCGTTCGTGTCCCCACAGCACGTTTCTTGGAGTAC"+`

`             "TCTACGTCTGAGTGTCATTTCTTCAATGGGACGGAGCGGGTGCGGTTCCTGGACAGATACT"+`

`             "TCCATAACCAGGAGGAGAACGTGCGCTTCGACAGCGACGTGGGGGAGTTCCGGGCGGTGAC"+`

`             "GGAGCTGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGACATCCTGGAAGACGAG"+`

`             "CGGGCCGCGGTGGACACCTACTGCAGACACAACTACGGGGTTGTGAGAGCTTCACCGTGCA"+ `

`             "GCGGCGAGACGCACTCGT";`

`       DNASequence query = new DNASequence(querySeq,`

`               AmbiguityDNACompoundSet.getDNACompoundSet());`

`       SubstitutionMatrix`<nucleotidecompound>` matrix = SubstitutionMatrixHelper.getNuc4_4();`

`       `

`       SimpleGapPenalty gapP = new SimpleGapPenalty();`

`       gapP.setOpenPenalty((short)5);`

`       gapP.setExtensionPenalty((short)2);`

`       `

`       SequencePair`&lt;DNASequence, NucleotideCompound&gt;` psa =`

`               Alignments.getPairwiseAlignment(query, target,`

`                       PairwiseSequenceAlignerType.LOCAL, gapP, matrix);`

`       System.out.println(psa);`

`   }`

AmbiguityDNA Compound Set allows not only ACTG, but also

ambiguity codes, also known as [IUB

Code](http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation)