Find in nucleotide files?

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.

/ Jonas

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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 ?

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 ?

Jim

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

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On 28-01-2008 at 18:16, James Procter <jimp@compbio.dundee.ac.uk> wrote:

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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

STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S
Tel: +45 3268 3268 - Fax: +45 3268 3868
serum@ssi.dk www.ssi.dk
  
This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you.

Thanks for putting up the example image, Jonas.

You've found a bug in the Find function. It won't find anything when doing a case-insensitive search in lower-case sequences, which is kind of annoying... to say the least, and not just restricted to dna. The workaround for the moment is to check the 'case sensitive' box when you search dna, and make sure that both the query and the dna is in lower case - or alternatively uppercase all the dna (see the edit submenu of the pop-up menu).

It'll be fixed in the development version in about half an hour...
Jim

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J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk

Ah! Excellent! Now the find works everywhere :slight_smile: Quick fix on the development version as well! Thanks a lot.
/ jonas

STATENS SERUM INSTITUT - 5, Artillerivej - DK-2300 Copenhagen S
Tel: +45 3268 3268 - Fax: +45 3268 3868
serum@ssi.dk www.ssi.dk
  
This e-mail, inclusive of attachments, is intended for the person(s) or entity stated above and may contain confidential information. Unauthorised reading, disclosure, copying, distribution or use of this information may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete your copy. Thank you.

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On 29-01-2008 at 10:11, James Procter <jimp@compbio.dundee.ac.uk> wrote:

Thanks for putting up the example image, Jonas.

You've found a bug in the Find function. It won't find anything when
doing a case-insensitive search in lower-case sequences, which is kind
of annoying... to say the least, and not just restricted to dna. The
workaround for the moment is to check the 'case sensitive' box when you
search dna, and make sure that both the query and the dna is in lower
case - or alternatively uppercase all the dna (see the edit submenu of
the pop-up menu).