[Jalview-discuss] Find in nucleotide files?

[Jonas Larsson]

>>> On 28-01-2008 at 18:16, James Procter <jimp at compbio.dundee.ac.uk> wrote:
> Jonas Larsson wrote:
>> Why is it that I can not search on sequences if they are nucleotides? If I 
> am working on amino acid sequences everything works OK but with nucleotides 
> it seems impossible. Have anyone else had this problem as well? I simply get 
> no results or a "0 matches found" found every time.

> what version are you using, Jonas ?

2.3 May 24, I also tried with the Web start version directly from the web page (2.3 May 10). Same behaviour in both. Java 1.6.0_03-b05
 
> It seems to work fine with the current version available from the 
> website. The find function tries to be slightly intelligent so it might 
> be matching on sequence ID, sequence position or sequence string 
> (excluding gaps and optionally matching case). Can you show it doesn't 
> work for a really simple case ?

This is as simple as it gets. http://www.e-tintin.com/test_find.png 

In the top part trying to find in the nucleotide sequence and in the bottom one in the protein one. For simplicity sake I used the find all, but the result is the same regardless of that.

/ Jonas
-- 

Jonas Larsson, M.Sc. Ph.D.
Bacterial Typing
Department of Bacteriology, Mycology & Parasitology
Statens Serum Institut
Bygning 37b, 133
Artillerivej 5
2300 Copenhagen S
Denmark
Phone: (+45) 3268 3221    Fax: (+45) 3268 3868



 
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