[Biojava-l] Biojava-l Digest, Vol 125, Issue 2

[Khalil El Mazouari]

Hi Andreas,

thanks for the feedback.

increasing gop and gep was not sufficient. I had to use a modified version of nuc-4_2 scoring matrix where I set the mismatch value very low. This solved the problem,

Best

khalil




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On 11 Jun 2013, at 18:00, biojava-l-request at lists.open-bio.org wrote:

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>   1. Re: Local aln - contig assembly (Andreas Prlic)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Mon, 10 Jun 2013 17:47:41 -0700
> From: Andreas Prlic <andreas at sdsc.edu>
> Subject: Re: [Biojava-l] Local aln - contig assembly
> To: Khalil El Mazouari <khalil.elmazouari at gmail.com>
> Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> Message-ID:
> 	<CALthepyva-+rAoP=8yH=OmDeA1S7i9Ov4js5eAYk-BL4r1Xang at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Khalil,
> 
> if you can get 100% sequence ID depends on your sequences.. you can try to
> enforce a more strict alignment by increasing the gap penalties
> significantly (try to double or triple gap opening and extension) .
> 
> A
> 
> 
> On Sun, Jun 9, 2013 at 12:32 PM, Khalil El Mazouari <
> khalil.elmazouari at gmail.com> wrote:
> 
>> 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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