Thank Andreas,
these 2 seq (s1 and s2) are exactly the same. Indeed, it works for 100%
identical seq.
I have used the same code as below except, I used .GLOBAL. I am not interested
in local alignment.
Regards,
Khalil
On 19 Jan 2011, at 16:07, Andreas Prlic wrote:
> Hi Kalil,
>
> can you send your code snipplet that you are running? I just re-ran
> the cookbook example and it works for me. Also this behaves fine:
>
> ProteinSequence s1 = new
> ProteinSequence("QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR");
> ProteinSequence s2 = new
> ProteinSequence("QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSSQVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCAR");
>
> SubstitutionMatrix<AminoAcidCompound> matrix = new
> SimpleSubstitutionMatrix<AminoAcidCompound>();
> SequencePair<ProteinSequence, AminoAcidCompound> pair =
> Alignments.getPairwiseAlignment(s1, s2,
> PairwiseSequenceAlignerType.LOCAL, new
> SimpleGapPenalty(), matrix);
> System.out.printf("%n%s vs %s%n%s",
> pair.getQuery().getAccession(),
> pair.getTarget().getAccession(), pair);
>
> System.out.println("Identicals:" + pair.getNumIdenticals());
> System.out.println("Similars:" + pair.getNumSimilars());
>
> Andreas
>
>
>
> On Wed, Jan 19, 2011 at 2:39 AM, Khalil El Mazouari
> <[email protected]> wrote:
>> Hi all,
>>
>> while doing PSA or MSA with default gop and gep values I obtained the
>> following alignment!
>>
>> QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS
>> QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA---------------------R
>>
>> Expected PSA should be at least
>> QVQLQQPGSELVKPGASVKLSCKASGYTFTNYLIHWVRQRPGRGLEWIGRIDPNSGGTKYSEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCATYYFGRSFFDFWGQGTTLTVSS
>> QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCA-----R----------------
>>
>> this expected alignment was obtained with gop=1 and gep=100
>>
>> I can't understand while the PSA algorithm with default values always adds
>> many gaps at the end of alignment to end up with a S:R while it is obvious
>> that with less gaps we could obtain better SequencePair with R:R?
>>
>> Finally, how to get a score for PSA, that reflects the number of identical,
>> similar residues and gaps?
>>
>> Many thanks.
>>
>> Khalil
>>
>>
>>
>> _______________________________________________
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>>
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