CDS Translation for DNA blasts - How to Blast 2 DNA sequences with amino acid translations? (Jun/04/2008 )

Greetings everyone,

I recently ran into a problem. I have been using the following site to Blast 2 DNA sequences against each other.

http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi?0

When I find a mutation in one sequence against my reference sequence, I conveniently click on "Show CDS translation" and then click on "align". This not only shows Blast results of the two sequences but also the Amino Acid translations of the DNA. However, now clicking the "show CDS translation " does not reveal the amino acid translations! I don't know why this is happening.

Am I doing something wrong? Is there a glitch in the website? Or could someone recommend another website for this purpose?

Thanks for your help.

-purplefetus-

QUOTE (purplefetus @ Jun 5 2008, 01:37 AM)

Is there a glitch in the website?

Or could someone recommend another website for this purpose?

Thanks for your help.

Which sequences are you working on?

-dalloliogm-

I'm working on the gene FMO3. It's the causative gene of the disease TMAU (Trimethylamineurea). I'm extracting leukocytic DNA from whole blood and using that for PCR amplifications. The purified products get sequenced.

-purplefetus-

Doing the BLASTs of 2 sequences against each other with the first being my experimental and 2nd being the GI # of the FMO3 gene was very convenient as the reading frame was automatically calibrated to the sequence with the GI #. Therefore the amino acid translations were correct to the human protein FMO3.

Is my computer the only one thats no longer giving the CDS translation? I still can't get this to work right and I used to this for the past couple years! I don't know why it's not working anymore. Can anyone else verify this?

Hoping to get some feedback from ya all.
Thanks

-purplefetus-

hi purplefetus,

i used the blast2sequence program often to compare a treatment i had in my experiments. i never used the translate cds function, so i couldn't tell you whether it's working now or it's not. however, i can recommend you to use another program to translate your sequence. there's an emboss program called sixpack, you can google it, it gives you the six reading frames of the input sequence, if there's any mutation that is affecting you could detect it by doing the alignment with the aminoacid sequences rather than the DNA. i hope this helps. best wishes.

tj.

-toejam-