[Biojava-l] Multiple sequence alignment in BioJava

[Andreas Prlic]

Hi Alastair,

BioJava 1.X can do distributions, however there is no counterpart for
this yet in BioJava 3.

Andreas

On Wed, Apr 6, 2011 at 9:40 AM, Alastair Kilpatrick
<alastair.m.kilpatrick at googlemail.com> wrote:
> Thanks - I had just downloaded the BioJava jars manually so that's
> fixed the CookBook code. However, I've made some changes in order to
> align DNA sequences instead and am running into more errors - this
> code:
>
>        public static void main(String[] args) {
>                String[] seqs = {"GATTACATTT", "CGATTACATG", "ATGGATTACA"};
>                List<DNASequence> lst = new ArrayList<DNASequence>();
>                for(String seq : seqs) {
>                        lst.add(new DNASequence(seq));
>                }
>                Profile<DNASequence, NucleotideCompound> profile =
> Alignments.getMultipleSequenceAlignment(lst); //**
>                System.out.println(profile);
>                ConcurrencyTools.shutdown();
>        }
>
> gives:
> java.util.concurrent.ExecutionException: java.lang.NullPointerException
>        at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
>        at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
>        at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
>        at CookbookMSA.main(CookbookMSA.java:49)
>
> at the 'alignment' line (**) - not sure what the problem is here, I
> see that getMultipleSequenceAlignment() has an extra argument(s) in
> the Javadoc but these weren't required in the example?
> Final question (hopefully!) - once I have the alignments I require I'd
> like to create a sequence logo - is there a way of doing this in
> BioJava3? From a google search I've seen references to
> DistributionTools.distOverAlignment() and similar, but can't find
> anything like that in the new api.
>
> Thanks again, sorry everyone for all the questions!
>
> Alastair
>
>
> On 6 April 2011 12:09, Scooter Willis <willishf at gmail.com> wrote:
>>
>> You need to use the forester.jar file from the biojava3 code check out. If you are using maven this should be automatic.
>>
>> On Apr 6, 2011 5:07 AM, "Alastair Kilpatrick" <alastair.m.kilpatrick at googlemail.com> wrote:
>>
>> Dear all,
>> I'm pretty new to BioJava so I may be missing something - I've checked
>> through the list archives without much luck.
>> I've been trying to do some multiple sequence alignments but I've been
>> running into strange errors. To try and find where the problem is,
>> I've just copied the code straight from
>> http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
>> I'm still getting an error:
>>
>> Caused by: java.lang.ClassNotFoundException:
>> org.forester.phylogenyinference.DistanceMatrix
>>
>> It would seem that this is something to do with forester.jar, which I
>> had to download separately (from http://code.google.com/p/forester/)
>> as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
>> when I look through the jar in Eclipse, there isn't anything named
>> 'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
>> 'phylogeny.factories' and 'phylogeny.iterators'. Is there something
>> I'm doing wrong, or is it the case that either one of BioJava or
>> forester has been updated and things have broken somewhere (I see the
>> CookBook page was updated in July 2010 but forester was updated just
>> last month)? Either way, any ideas would be much appreciated!
>>
>> Many thanks,
>> Alastair Kilpatrick
>>
>> PhD candidate,
>> School of Informatics, University of Edinburgh
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>
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