[Biojava-dev] Near Matches

[Schreiber, Mark]

Hi -

I think Matthew checked in something that does what you want a few days back. Have a look at the list archives, or cvs records for that last few weeks.

- Mark


-----Original Message-----
From: Osborne, John [mailto:jko1 at cdc.gov] 
Sent: Friday, 12 September 2003 6:20 a.m.
To: biojava-dev at biojava.org
Subject: [Biojava-dev] Near Matches


Hi,

I am looking for a way in Biojava to iterate quickly through a list of DNA N-mers for sequences that are almost an exact match, like 23 of 25 bases.  The mismatches can occur in ANY position in a sequence.  Other than iterating through a SymbolList and keeping track of the number of mismatches, is there a better (read faster) way to do this?  I was thinking maybe the SuffixTree class, but since sequence order is unimportant it doesn't see like the right tool for the job.

Right now it is going to be a little bit ugly, since I am putting this into a O(n^2) function with a big n...

 -John
_______________________________________________
biojava-dev mailing list
biojava-dev at biojava.org http://biojava.org/mailman/listinfo/biojava-dev
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================