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Internal stop codons in protein sequences

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

fasta sequence
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updated by Ram Ram • written by vivekananthrp • vivekananthrp

2 answers

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

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written by Brian Bushnell Brian Bushnell

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.

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written by harold.smith.tarheel harold.smith.tarheel

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