[Biojava-dev] Case sensitivity in Alignment

[Andreas Prlic]

The problem is that the substitution matrices are all upper case. We can
probably fix this by making the NucleotideCompound.equals method case
insensitive...

Does anybody see an issue with that?

A


On Wed, Nov 20, 2013 at 8:22 AM, Michael Heuer <heuermh at gmail.com> wrote:

> Hello Andreas, David
>
> Lower case is the convention for soft-masking sequences from alignment
>
> http://www.ncbi.nlm.nih.gov/books/NBK1763/
>
> http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.Create_a_masked_BLAST
>
> If we are using this convention, perhaps it should be more clearly
> documented.  What happens if you use mixed case?
>
>    michael
>
>
> On Wed, Nov 20, 2013 at 5:29 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> > Hi David,
> >
> > not sure if we should consider this a bug or a feature: It should be easy
> > to work around this by calling toUppercase on your strings. We could of
> > course internally convert all nucleotides to upper case, but that would
> > remove the possibility for people to use mixed upper case and lower case
> > sequences to represent e.g. alignment conservation.
> >
> > Any opinions by other people on this? Is anybody using mixed case
> sequences?
> >
> > Andreas
> >
> >
> > On Mon, Nov 18, 2013 at 11:43 AM, Waring, David A <dwaring at fhcrc.org>
> wrote:
> >
> >>
> >> There seems to be a bug in the alignment package. If DNA sequences are
> >> created using lower case letters, the alignment methods don't work.
> Looks
> >> like the the default substitution matrix is coded in upper case, and the
> >> underlying case of the DNA sequence is being used in the alignment.
> Seems
> >> like a bug to me.
> >>
> >>  This problem occurs when the DNA Sequence is create either using the
> >> DNASequence constructor, or reading from a fasta which is in lower case.
> >>
> >>
> >> The code below shows the problem.
> >>
> >>
> >>     static SimpleGapPenalty gapP;
> >>     static SubstitutionMatrix<NucleotideCompound> matrix;
> >>
> >>     public static void main(String[] args)throws Exception{
> >>        matrix = SubstitutionMatrixHelper.getNuc4_4();
> >>         gapP = new SimpleGapPenalty();
> >>         gapP.setOpenPenalty((short)5);
> >>         gapP.setExtensionPenalty((short)2);
> >>         testHardcoded();
> >>     }
> >>
> >>     public static void testHardcoded()throws Exception{
> >>        Sequence<NucleotideCompound> seq1 = new
> >> DNASequence("AGGGCTTTACCCCGGTTAA");
> >>         Sequence<NucleotideCompound> seq2 = new
> >> DNASequence("ACCCCGGTTTAATATTTTT");
> >>         Sequence<NucleotideCompound> seq3 = new
> >> DNASequence("agggctttaccccggttaa");
> >>         Sequence<NucleotideCompound> seq4 = new
> >> DNASequence("accccggtttaatattttt");
> >>         alignPair(seq1,seq2);
> >>         alignPair(seq1,seq4);
> >>         alignPair(seq3,seq4);
> >>
> >>     }
> >>
> >>
> >>     public static void alignPair(Sequence<NucleotideCompound> seq1,
> >> Sequence<NucleotideCompound> seq2){
> >>                 SequencePair<Sequence<NucleotideCompound>,
> >> NucleotideCompound> pair =
> >>                         Alignments.getPairwiseAlignment(seq1,seq2,
> >>                         Alignments.PairwiseSequenceAlignerType.GLOBAL,
> >> gapP, matrix);
> >>
> >>         System.out.printf("%s", pair);
> >>         System.out.println();
> >>     }
> >>
> >>
> >>
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> >>
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