[Biojava-l] K-mers
Andy Yates
ayates at ebi.ac.uk
Fri Oct 29 18:35:43 UTC 2010
So if it's a suffix tree that's quite a fixed data structure so the chances of developing a pluggable mechanism there would be hard. I think there also has to be a limit as to what we can sensibly do. If people want to contribute this kind of work though then it's all be very well received (with the corresponding test environment/cases of course).
Cheers,
Andy
On 29 Oct 2010, at 17:56, Mark Fortner wrote:
> It might be useful to make the K-mer storage mechanism pluggable. This
> would allow a developer to use anything from a simple MultiMap, to a NoSQL
> key-value database to store K-mers. You could plugin custom map
> implementations to allow you to keep a count of the number of instances of
> particular K-mers that were found. It might also be useful to be able to do
> set operations on those K-mer collections. You could use it to determine
> which K-mers were present in a pathogen and not in a host.
> http://www.ncbi.nlm.nih.gov/pubmed/20428334
> http://www.ncbi.nlm.nih.gov/pubmed/16403026
>
> Cheers,
>
> Mark
>
> card.ly: <http://card.ly/phidias51>
>
>
> On Fri, Oct 29, 2010 at 9:27 AM, Vishal Thapar <vishalthapar at gmail.com>wrote:
>
>> Hi Andy,
>>
>> This is good to have. I feel that including it as a part of core may not be
>> necessary but having it as part of Genomic module in biojava3 will be nice.
>> There is a project Bioinformatica
>>
>> http://code.google.com/p/bioformatica/source/browse/#svn/trunk/src/bioformatica/sequencewhich
>> does something similar although not exactly. It counts the k-mers in a
>> given fasta file but it does not count k-mers for each sequence within the
>> file, just all within a file. This is a good feature to have specially if
>> one is trying to find patterns within sequences which is what I am trying
>> to
>> do. It would most certainly be helpful to have a k-mer counting algorithm
>> that counts k-mer frequency for each sequence. The way to go would be to
>> use
>> suffix trees. Again I don't know if biojava has a suffix tree api or not
>> since I haven't used java in a while and am just switching back to it. A
>> paper on using suffix trees to generate genome wide k-mer frequencies is:
>> http://www.biomedcentral.com/1471-2164/9/517/abstract (kurtz et al,
>> software
>> is tallymer). It would be some work to implement this in java as a module
>> for biojava3 but I can see that this will be helpful. Again, for small
>> fasta
>> files, it might not be efficient to create a suffix tree but for bigger
>> files, I think that might be the way to go.
>>
>> Thats just my two cents.What do you think?
>>
>> -vishal
>>
>> On Fri, Oct 29, 2010 at 4:12 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>>
>>> Hi Vishal,
>>>
>>> As far as I am aware there is nothing which will generate them in BioJava
>>> at the moment. However it is possible to do it with BioJava3:
>>>
>>> public static void main(String[] args) {
>>> DNASequence d = new DNASequence("ATGATC");
>>> System.out.println("Non-Overlap");
>>> nonOverlap(d);
>>> System.out.println("Overlap");
>>> overlap(d);
>>> }
>>>
>>> public static final int KMER = 3;
>>>
>>> //Generate triplets overlapping
>>> public static void overlap(Sequence<NucleotideCompound> d) {
>>> List<WindowedSequence<NucleotideCompound>> l =
>>> new ArrayList<WindowedSequence<NucleotideCompound>>();
>>> for(int i=1; i<=KMER; i++) {
>>> SequenceView<NucleotideCompound> sub = d.getSubSequence(
>>> i, d.getLength());
>>> WindowedSequence<NucleotideCompound> w =
>>> new WindowedSequence<NucleotideCompound>(sub, KMER);
>>> l.add(w);
>>> }
>>>
>>> //Will return ATG, ATC, TGA & GAT
>>> for(WindowedSequence<NucleotideCompound> w: l) {
>>> for(List<NucleotideCompound> subList: w) {
>>> System.out.println(subList);
>>> }
>>> }
>>> }
>>>
>>> //Generate triplet Compound lists non-overlapping
>>> public static void nonOverlap(Sequence<NucleotideCompound> d) {
>>> WindowedSequence<NucleotideCompound> w =
>>> new WindowedSequence<NucleotideCompound>(d, KMER);
>>> //Will return ATG & ATC
>>> for(List<NucleotideCompound> subList: w) {
>>> System.out.println(subList);
>>> }
>>> }
>>>
>>> The disadvantage of all of these solutions is that they generate lists of
>>> Compounds so kmer generation can/will be a memory intensive operation.
>> This
>>> does mean it has to be since sub sequences are thin wrappers around an
>>> underlying sequence. Also the overlap solution is non-optimal since it
>>> iterates through each window rather than stepping through delegating onto
>>> each base in turn (hence why we get ATG & ATC before TGA)
>>>
>>> As for unique k-mers that's something which would require a bit more
>>> engineering & would be better suited to a solution built around a Trie
>>> (prefix tree).
>>>
>>> Hope this helps,
>>>
>>> Andy
>>>
>>> On 28 Oct 2010, at 18:40, Vishal Thapar wrote:
>>>
>>>> Hi All,
>>>>
>>>> I had a quick question: Does Biojava have a method to generate k-mers
>> or
>>>> K-mer counting in a given Fasta Sequence / File? Basically, I want
>> k-mer
>>>> counts for every sequence in a fasta file. If something like this
>> exists
>>> it
>>>> would save me some time to write the code.
>>>>
>>>> Thanks,
>>>>
>>>> Vishal
>>>> _______________________________________________
>>>> Biojava-l mailing list - Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>> --
>>> Andrew Yates Ensembl Genomes Engineer
>>> EMBL-EBI Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> *Vishal Thapar, Ph.D.*
>> *Scientific informatics Analyst
>> Cold Spring Harbor Lab
>> Quick Bldg, Lowe Lab
>> 1 Bungtown Road
>> Cold Spring Harbor, NY - 11724*
>> _______________________________________________
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>>
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--
Andrew Yates Ensembl Genomes Engineer
EMBL-EBI Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
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