[Biojava-l] SimpleGapPenalty defaults

[Khalil El Mazouari]

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
> <khalil.elmazouari at gmail.com> 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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