See http://java.sun.com/j2se/1.3/docs/guide/serialization/relnotes.html
The only reason I know this is I had this problem before, too ( :
Moses
On Tuesday, January 7, 2003, at 02:28 PM, Schreiber, Mark wrote:
Hi -
If you already have the SimpleGene features constructed these will
contain a Location object. However, I think you are saying how can I
find a subsequence in my Genomic sequence and locate the gene that way?
To rapidly find exact matches you can use the biojava
KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
It contains a main method that demonstrates it's use. This is a very
efficient algorithm for finding exact matches.
Note: if the genome is larger than 64kb you will not be able to dump it
as a String as that is the maximum String length. You could dump it as a
char[].
- Mark
-----Original Message----- From: Karin Lagesen [mailto:[EMAIL PROTECTED]] Sent: Tuesday, 7 January 2003 10:53 p.m. To: [EMAIL PROTECTED] Subject: [Biojava-l] locating genes in a genomic sequenceHi! I am trying to build a small program for finding intergenic areas. This I am planning to do by locating all mRNA's in a genome and outputting all the areas inbetween. Biojava seems to be able to help with most of my tasks. However, I have a few questions. From what I have understood I can have the genomic sequence as a SimpleSequence with all of the genes as SimpleGene's attached via a FeatureHolder to the genomic sequence. However, I have not figured out a smart way of finding the location of each of the genes in the genomic sequence. Since genomic sequences can be large, I hoped to avoid having to dump the sequence in a string and use indexOf(gene sequence) to find the position. Is there something I am missing here, or have I just misunderstood all of this? Thankyou in advance for your help. Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l======================================================================= 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. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
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