[Biojava-l] Sequence Iteration in BioJava(x)

[mark.schreiber at novartis.com]

Actually orderNSymbolList gives overlapping NMers. windowedSymbolList 
gives non-overlapping Nmers.

given the sequence 

actcgcatgcgatcgcag


orderNSymbolList (with order of 4) would give

actc, ctcg, tcgc etc

windowedSymbolList with an order of 4 would give

actc, gcat, gcga, etc

eventually the windowedSymbolList woud actually throw an exception cause 
the sequence above is not evenly divisible by 4 (seq.length() % 4 != 0)

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
Sent by: biojava-l-bounces at portal.open-bio.org
12/16/2005 09:43 AM

 
        To:     "David Huen" <smh1008 at cam.ac.uk>, <m.fortner at sbcglobal.net>
        cc:     biojava-list <biojava-l at biojava.org>, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        RE: [Biojava-l] Sequence Iteration in BioJava(x)


orderNSymbolList splits the sequence into non-overlapping chunks. What
is required here is chunks that are only one base different (further on)
than the previous chunk.

The simplest way would be this:

                 SymbolList mySeq; // this is your sequence from somewhere 
else
                 for (int i = 1 ; i <= mySeq.length()-2; i++) {
                                 SymbolList trimer = mySeq.subSeq(i,i+2); 
// coords are
inclusive so i to i+2 = 3 bases
                                 // do something with your trimer here
                 }

Note that the index starts at 1 and goes right up to and including
length(), as symbols in a SymbolList are 1-indexed, not 0-indexed.
 
cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of David Huen
> Sent: Friday, December 16, 2005 7:34 AM
> To: m.fortner at sbcglobal.net
> Cc: biojava-list
> Subject: Re: [Biojava-l] Sequence Iteration in BioJava(x)
> 
> 
> On Dec 15 2005, Mark Fortner wrote:
> I think what you want is the SymbolListViews.orderNSymbolList method.
> 
> It will take a SymbolList and turn it into another where it 
> is viewed in 
> another compound alphabet of the required order.
> 
> 
> >I'm looking for the best way to iterate through all
> >nmers within a given sequence.  For example, given a
> >sequence that looks like this:
> >
> >ACTGACTGACTG
> >
> >If I extract all trimers from this I should get:
> >
> >ACT
> >CTG
> >TGA
> >GAC
> >ACT
> >CTG
> >TGA
> >GAC
> >ACT
> >CTG
> >
> >Is there an existing class that will allow me to
> >iterate through a sequence this way, or am I on my
> >own?
> >
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
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> 

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