Protocol Online logo
Top : Forum Archives: : Bioinformatics and Biostatistics

Deletion mutant protein prediction - (Jan/21/2008 )

Hello All,

I am trying to predict a protein (amino acid) sequence of the deleted gene. Any idea how to do that?

Detailed explanation of the question-

The deletion in the gene of my interest has been recently isolated. I would like to know if that deletion (which deletes one full exon and 2 exons partially and the introns within) creates a null protein by causing a stop mutation somewhere. All the exons in this gene have different reading frames so its difficult to put all exons together and read the sequence (may be this is limitation of DNAStrider that I am using) but I was wondering if I should take into account intronic region as well while this prediction. All I want to check is how the truncated protein looks like, if it creates any premature stop codon or it just keeps on reading till the end.
Anybody has any idea on how this can be worked out?

Thanks in advance.

-Jiang M-

so you only want to do a prediction, not a detailed experiment to verify experimentally that there is no protein?
if that is what you want to do, if i understand well your question you isolated the gene of interest with the deletion so you should have the sequence (in nucleotides) right? if that is so, you can use a program called "sixpack" which gives you the six reading frames of the whole sequence indicating with a * the stop codons. i would only use the exons.


QUOTE (rodpck @ Jan 21 2008, 05:38 PM)
i would only use the exons.

Even if the deletion starts in the intron and ends in exon?

-Jiang M-

ok ok, i think i get what you mean. i think you should consider also puting the introns as well to get the whole mRNA and then you can get the translation of the whole fragment and detect if it has any stop codons. does it have splicing? if it does that's what i meant when i said i would only use the exons and see if it is a functional protein or a transcript that could be degraded or no transcript at all. hope this helps.