| title | BioJava:CookBook3:PSA DNA |
|---|---|
| permalink | wiki/BioJava%3ACookBook3%3APSA_DNA |
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`<DNASequence, NucleotideCompound>` 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