Re: Biojava3 pairwise aligner result is different emboss' needle
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CALthepync=1hrzv_N7CQm9ggmAzxco8-WtHWco9rhwjhLqY0mw@mail.gmail.com> |
Hi, looks like the emboss' alignment is not penalising end gaps. You could try to use the smith waterman algorithm instead... Andreas On Wed, Mar 7, 2012 at 6:33 PM, 오정수 <[email protected]> wrote: > Hello > My name is Oh jeongsu, I am a student at Chungbuk National University in > korea. > > I've been run global alignments with biojava and needle. but biojava3 > pairwise aligner result is different emboss' needle. > > here my option and code >>query > AAAAAGAATAACAATTGGAAACGATTGCTAATACTTTATATGCTGAGAAGTTAAACGGATTACCGCCTAAAGAATGAGCTTGCGTCTGATTAGCTAGTTGGTAAGGTAAAAGCTTACCAAGGCAATTGTCAGTAGTTGGTCTGAGAGGATGATCAACCACACTGGGACTGAGACACGGCCCAG >>target > AACGCTGGCGGCAGGCTTAACACATGCAAGTCGAGCGCATCCTTCGGGGTGAGCGGCGGACGGGTTAGTAACGCGTGGGAACGTACCCTTTCTAAGGAATAATCATTGGAAATGATGACTAATACCTTATACGCCCTTTGGGGGAAAGATTTATCGGAGAAGGATCGGCCCGCGTTAGATTAGATAGTTGGTGGGGTAATGGCCTACCAAGTCTACGATCTATAGCTGGTTTTAGAGGATGATCAGCAACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGCGCAAGCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGTCTTAGGATCGTAAAGCTCTTTCGCTGGGGAAGATAATGACTGTACCCAGTAAAGAAGTCCCGGCTAACTCCGTGC > > Gap opening penalty : -10 > Gap extension penalty : -0.5 > > SubstitutionMatrix : biojava - nuc4_4 , needle - ednafull > > biojava result > query > AA-------------------------------------------------------------------------------------------AAAGAATAACAATTGGAAACGATTGCTAATACTTTATATGC----TGAG---AAG-TTAAACGGATTACCGCCTAAAGAATGA---GCTTGCGTCTGATTAGCTAGTTGGTAAGGTAAAAGCTTACCAAGGCAATTGTCAGTAGTTGGTCTGAGAGGATGATCAACCACACTGGGACTGAGACACGGCCCAG------------------------------------------------------------------------------------------------------------------------------------------------------------ > target > AACGCTGGCGGCAGGCTTAACACATGCAAGTCGAGCGCATCCTTCGGGGTGAGCGGCGGACGGGTTAGTAACGCGTGGGAACGTACCCTTTCTAAGGAATAATCATTGGAAATGATGACTAATACCTTATACGCCCTTTGGGGGAAAGATTTATCGGA------------GAAGGATCGGCCCGCGTTAGATTAGATAGTTGGTGGGGTAATGGCCTACCAAGTCTACGATCTATAGCTGGTTTTAGAGGATGATCAGCAACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGCGCAAGCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGTCTTAGGATCGTAAAGCTCTTTCGCTGGGGAAGATAATGACTGTACCCAGTAAAGAAGTCCCGGCTAACTCCGTGC > > needle result > query > -------------------------------------------------------------------------------AA------------AAAGAATAACAATTGGAAACGATTGCTAATACTTTATATGC----TGAG---AAG-TTAAACGGATTACCGCCTAAAGAATGAGCTTGCGTCTGATTAGCTAGTTGGTAAGGTAAAAGCTTACCAAGGCAATTGTCAGTAGTTGGTCTGAGAGGATGATCAACCACACTGGGACTGAGACACGGCCCAG------------------------------------------------------------------------------------------------------------------------------------------------------------ > target > AACGCTGGCGGCAGGCTTAACACATGCAAGTCGAGCGCATCCTTCGGGGTGAGCGGCGGACGGGTTAGTAACGCGTGGGAACGTACCCTTTCTAAGGAATAATCATTGGAAATGATGACTAATACCTTATACGCCCTTTGGGGGAAAGATTTATCGGA---------GAAGGATCGGCCCGCGTTAGATTAGATAGTTGGTGGGGTAATGGCCTACCAAGTCTACGATCTATAGCTGGTTTTAGAGGATGATCAGCAACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGCGCAAGCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGTCTTAGGATCGTAAAGCTCTTTCGCTGGGGAAGATAATGACTGTACCCAGTAAAGAAGTCCCGGCTAACTCCGTGC > > > i want to same result , could you tell me what is wrong? > > thansks > > Oh jeongsu _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l