[Biojava-l] Biojava3 pairwise aligner result is different emboss' needle

[Andreas Prlic]

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 <misojs at gmail.com> 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