Internal stop codons in protein sequences

Question

[vivekananthrp]

Hi, there are protein sequences with internal stop codons (* in between).

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

Answer 1

[Brian Bushnell]

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

Answer 2

[harold.smith.tarheel]

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.