Richard,
Thanks for the example. Your approach is very similar to a non-BioJava
approach that I had worked out earlier. I was wondering if the
BioJava(x) API provides any performance benefit over simply running a
window along a character stream?
The work that we're doing involves iterating through the human genome,
(and in a number of cases, metagenomic sequences) and we're trying to
squeeze as much performance out of it as possible while minimizing the
memory footprint.
Thanks,
Mark
Richard HOLLAND wrote:
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of David Huen
Sent: Friday, December 16, 2005 7:34 AM
To: [EMAIL PROTECTED]
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?
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