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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