[Biojava-dev] Protein Alignment Exception
Chris Friedline
cfriedline at vcu.edu
Tue Dec 7 17:11:55 UTC 2010
Hi John,
I do this all the time and at (very) quick glance your code looks fine from
what I can remember about the legacy 1.7.1 codebase. However, when I did
it, I normally loaded from external substitution matrix files (downloaded
from NCBI) and used the PROTEIN-TERM alphabet.
You might also want to get going with the BioJava3 libraries. I'm seeing a
pretty big boost in performance now with beta2 and less code (~11k/sec on 8
CPUs).
I also had some issues a while back with BioJava 1.7.1 and protein
alignments that were fixed in the subversion repo, but not made part of the
main binary release on biojava.org. You might want to download and compile
the 1.7.1 dev version and try those libraries, as well. There are some
changes that haven't made it into the wiki with the dev version 1.7.1 (as I
recall), but it's pretty straightforward to get it to work almost like what
you have below.
Chris
On Tue, Dec 7, 2010 at 11:26 AM, John Hawkins <
john.hawkins at biotec.tu-dresden.de> wrote:
> Hi All,
>
> I have searched the archives of this list to try and solve my problem
> and I can not find an answer.
>
> I am attempting to use BioJava to perform some pairwise alignments of
> protein sequences.
>
> I have written a simple test class to check the functionality, and I am
> getting an exception which does not make sense to me.
>
> Using the code below I receive the Exception
>
> org.biojava.bio.BioRuntimeException: Alphabet missmatch occured:
> sequences with different alphabet cannot be aligned.
> at
>
> org.biojava.bio.alignment.NeedlemanWunsch.pairwiseAlignment(NeedlemanWunsch.java:635)
> at utilities.PairWiseAlignment.alignProteins(PairWiseAlignment.java:68)
> at utilities.PairWiseAlignment.main(PairWiseAlignment.java:184)
>
> This is occuring even when I input two identical protein sequences (as
> Strings).
> It appears that the ProteinTools.createProteinSequence method generates
> a unique alphabet for each sequence it is given,
> and I cannot see any way to force the resulting sequence to have the
> same underlying alphabet.
>
> Please forgive me I have overlooked something obvious.
>
> Regards
> John Hawkins
>
> ----------------------------------------------------------------------------------------------------------------------------
> package utilities;
>
> import org.biojava.bio.alignment.NeedlemanWunsch;
> import org.biojava.bio.alignment.SequenceAlignment;
> import org.biojava.bio.alignment.SmithWaterman;
> import org.biojava.bio.alignment.SubstitutionMatrix;
> import org.biojava.bio.seq.ProteinTools;
> import org.biojava.bio.seq.Sequence;
> import org.biojava.bio.symbol.AlphabetManager;
> import org.biojava.bio.symbol.FiniteAlphabet;
>
>
> public class PairWiseAlignment {
>
> private int score;
> private int score2;
> private String aln1;
> private String aln2;
>
> public PairWiseAlignment(int score, int score2, String aln1,
> String aln2) {
> super();
> this.score = score;
> this.score2 = score2;
> this.aln1 = aln1;
> this.aln2 = aln2;
> }
>
>
> /** This performs an alignment of two given sequences and
> * returns the result in an object.
> *
> * @param seq1 a query sequence
> * @param seq2 a target sequence
> */
> public static PairWiseAlignment alignProteins(String seq1, String
> seq2) {
> int score = 0;
> int score2 = 0;
> String aln1= "";
> String aln2= "";
> try {
> // The alphabet of the sequences. For this example DNA is choosen.
> FiniteAlphabet alphabet = (FiniteAlphabet)
> AlphabetManager.alphabetForName("PROTEIN");
> // Read the substitution matrix file.
> // For this example the matrix NUC.4.4 is good.
> SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet,
> PairWiseAlignment.getSubstitutionMatrix(), "BLOSUM62");
> // Define the default costs for sequence manipulation for the
> global alignment.
> SequenceAlignment aligner = new NeedlemanWunsch(
> (short) 0, // match
> (short) 3, // replace
> (short) 2, // insert
> (short) 2, // delete
> (short) 1, // gapExtend
> matrix // SubstitutionMatrix
> );
> Sequence query = ProteinTools.createProteinSequence(seq1,
> "query");
> Sequence target = ProteinTools.createProteinSequence(seq2,
> "target");
>
> System.err.println("ALPHA 1: " + query.getAlphabet() );
> System.err.println("ALPHA 2: " + target.getAlphabet() );
>
> // Perform an alignment and save the results.
> score = aligner.pairwiseAlignment(
> query, // first sequence
> target // second one
> );
> // Print the alignment to the screen
> aln1 = "Global alignment with Needleman-Wunsch:\n" +
> aligner.getAlignmentString();
>
> // Perform a local alginment from the sequences with
> Smith-Waterman.
> // Firstly, define the expenses (penalties) for every single
> operation.
> aligner = new SmithWaterman(
> (short) -1, // match
> (short) 3, // replace
> (short) 2, // insert
> (short) 2, // delete
> (short) 1, // gapExtend
> matrix // SubstitutionMatrix
> );
> // Perform the local alignment.
> score2 = aligner.pairwiseAlignment(query, target);
>
> aln2 = "\nlocal alignment with SmithWaterman:\n" +
> aligner.getAlignmentString();
> } catch (Exception exc) {
> exc.printStackTrace();
> }
>
> return new PairWiseAlignment(score, score2, aln1, aln2);
>
> }
>
> public static String getSubstitutionMatrix() {
> //TODO: Load this as a resource
> String result = "# Matrix made by matblas from
> blosum62.iij \n" +
> "# * column uses minimum score\n" +
> "# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units\n" +
> "# Blocks Database = /data/blocks_5.0/blocks.dat\n" +
> "# Cluster Percentage: >= 62\n" +
> "# Entropy = 0.6979, Expected = -0.5209\n" +
> " A R N D C Q E G H I L K M F P S T W Y
> V B Z X \n" +
> "A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2
> 0 -2 -1 0 \n" +
> "R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2
> -3 -1 0 -1 \n" +
> "N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2
> -3 3 0 -1 \n" +
> "D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3
> -3 4 1 -1 \n" +
> "C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2
> -1 -3 -3 -2 \n" +
> "Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1
> -2 0 3 -1 \n" +
> "E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2
> -2 1 4 -1 \n" +
> "G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3
> -3 -1 -2 -1 \n" +
> "H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2
> -3 0 0 -1 \n" +
> "I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1
> 3 -3 -3 -1 \n" +
> "L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1
> 1 -4 -3 -1 \n" +
> "K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2
> -2 0 1 -1 \n" +
> "M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1
> 1 -3 -1 -1 \n" +
> "F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3
> -1 -3 -3 -1 \n" +
> "P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3
> -2 -2 -1 -2 \n" +
> "S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2
> -2 0 0 0 \n" +
> "T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2
> 0 -1 -1 0 \n" +
> "W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2
> -3 -4 -3 -2 \n" +
> "Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7
> -1 -3 -2 -1 \n" +
> "V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1
> 4 -3 -2 -1 \n" +
> "B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3
> -3 4 1 -1 \n" +
> "Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2
> -2 1 4 -1 \n" +
> "X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1
> -1 -1 -1 -1 ";
>
> return result;
> }
>
>
> public static void main (String args[]) {
> String seq1=
>
> "RRRVTVRKADAGGLGISIKGGRENKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKYMK";
> String seq2=
>
> "LGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAN";
> PairWiseAlignment test = PairWiseAlignment.alignProteins(
> seq2, seq2 ) ;
> System.err.println("SCORE 1: " + test.score + "\n" +
> test.getAln1() + "\n");
> System.err.println("SCORE 2: " + test.score2 + "\n" +
> test.getAln2() + "\n");
> }
>
>
> public int getScore() {
> return score;
> }
>
>
> public void setScore(int score) {
> this.score = score;
> }
>
>
> public int getScore2() {
> return score2;
> }
>
>
> public void setScore2(int score2) {
> this.score2 = score2;
> }
>
>
> public String getAln1() {
> return aln1;
> }
>
>
> public void setAln1(String aln1) {
> this.aln1 = aln1;
> }
>
>
> public String getAln2() {
> return aln2;
> }
>
>
> public void setAln2(String aln2) {
> this.aln2 = aln2;
> }
> }
>
>
> -------------------------------------------------------------------------------------------------------
>
>
> --
>
> Dr John Hawkins
> Post-Doctoral Researcher
>
> Technische Universität Dresden
> Biotechnology Center
> Tatzberg 47/49
> 01307 Dresden
>
> Tel.: +49 (0) 351 463-40083
> Fax: +49 (0) 351 463-40087
> E-Mail: john.hawkins at biotec.tu-dresden
> Webpage: www.biotec.tu-dresden.de
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
--
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA
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