Question: Internal stop codons in protein sequences
0
gravatar for vivekananthrp
2.3 years ago by
vivekananthrp10 wrote:

Hi, there are protein sequences with internal stop codons ( '*' inbetween).

For example,

http://www.candidagenome.org/cgi-bin/protein/proteinPage.pl?dbid=CAL0000175821&seq_source=C.%20albicans%20SC5314%20Assembly%2022

What does these many internal stop codon means? While running bioinformatics predictions should I remove these '*'? Or should I remove these sequence from the fasta file before analysis?

Thanks in advance.

-Vivek Ananth

ADD COMMENTlink modified 2.3 years ago by harold.smith.tarheel4.3k • written 2.3 years ago by vivekananthrp10
3
gravatar for Brian Bushnell
2.3 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

That means the annotation is incorrect. The frame is wrong, or the sequence is wrong, or there isn't really a gene there.

ADD COMMENTlink written 2.3 years ago by Brian Bushnell16k
2
gravatar for harold.smith.tarheel
2.3 years ago by
United States
harold.smith.tarheel4.3k wrote:

No idea why the amino acid sequence is so full of errors but, if you download the DNA sequence and translate it yourself, it produces a single open reading frame. You may want to contact the webmaster at CGD about this problem.

FYI, I thought it might be due to the alternative genetic code used by Candida (both nuclear and mitochondrial genes contain variant codons), but that's not the explanation.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by harold.smith.tarheel4.3k
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