[Biojava-l] Local aln - contig assembly

[Khalil El Mazouari]

Hi,

I am trying to assemble overlapping sequence (direct & reverse) via local alignment. I am only searching for local aln with 100% identity.

Which parameters, matrix ... should I use in order to get 100% ident. local aln.

Any other suggestion for assembling overlapping seq (in Java) is welcome.

Thanks

khalil



   SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_2();
   SimpleGapPenalty gapP = new SimpleGapPenalty();
   gapP.setOpenPenalty((short) 5);
   gapP.setExtensionPenalty((short) 1);
   SequencePair<DNASequence, NucleotideCompound> psa =
   Alignments.getPairwiseAlignment(query, target,
   PairwiseSequenceAlignerType.LOCAL, gapP, matrix);




========

Local Alignment Identity: 97.84688995215312%

query     GGGGAAAACACGAAAGGCCCTTGGTGGAGGCGCTTGAGACGGTGACAAGGGTTCCCTGGC  68
          |||||| || |||  ||||||||||||||||||||||||||||||| |||||||||||||
target    GGGGAAGAC-CGATGGGCCCTTGGTGGAGGCGCTTGAGACGGTGACCAGGGTTCCCTGGC 417

query     CCCAGTAGTCAAAGGTCCGTGAGGAGCTCCACTTGTGTGCACAGTAATATGTGGCTGAGT 128
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
target    CCCAGTAGTCAAAGGTCCGTGAGGAGCTCCACTTGTGTGCACAGTAATATGTGGCTGAGT 477

query     CCACAGGGTCCATGTTGGTCATTGTAAGGACCACCTGGTCTTTGGAGGTGTCCTTGGTGA 188
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
target    CCACAGGGTCCATGTTGGTCATTGTAAGGACCACCTGGTCTTTGGAGGTGTCCTTGGTGA 537

query     TGGTGAGCCTGCTCTTCAGAGATGGGCTGTAGCGCTTATCATCATTCCAATAAATGAGTG 248
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
target    TGGTGAGCCTGCTCTTCAGAGATGGGCTGTAGCGCTTATCATCATTCCAATAAATGAGTG 597

query     CAAGCCACTCCAGGGCCTTTCCTGGGGGCTGACGGATCCAGCCCACACCCACTCCACTAG 308
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
target    CAAGCCACTCCAGGGCCTTTCCTGGGGGCTGACGGATCCAGCCCACACCCACTCCACTAG 657

query     TGCTGAGTGAGAACCCAGAGAAGGTGCAGGTCAGCGTGAGGGTCTGTGTGGGTTTCACCA 368
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
target    TGCTGAGTGAGAACCCAGAGAAGGTGCAGGTCAGCGTGAGGGTCTGTGTGGGTTTCACCA 717

query     GCGTAGGACCAGACTCCTTCAAGGTGATCTGGGCCATGGCCGGCTGGGCCGCGAGTAA 426
          |||||||||||||||||||||||||| ||||||||| |||||||||| |||| |||||
target    GCGTAGGACCAGACTCCTTCAAGGTG-TCTGGGCCA-GGCCGGCTGG-CCGCAAGTAA 772










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