stop codon identification

Question

[harpreetmanku04]

hello, i am working on genomics area... i am facing a problem on the identification of stop codons. how can i find in silico stop codons from a cds sequences?

[Martombo]

well if you have a coding sequence, the stop codon is by definition at the end of such sequence. maybe it would be easier if you describe better what data you have and what you want to get.

Answer 1

[Ibrahim Tanyalcin]

Dear,

You can do this using I-PV (http://i-pv.org/). I will give an example from myosin which is one of the example on the site ( http://i-pv.org/MYOSIN2.html ). Using this tool it is possible to view the distribution of nonsynonymous mutations that has resulted in a stop codon. Alternatively you can click on any of the amino acids and see if there is a theoretically possible point mutation that can result in a stop codon.

Below video first shows the distribution of stop codons plotted from a variation file, you can click on these and it will take you to the corresponding dbSNP website; the second part shows 9 possible point mutations that can occur in a given amino acid (lysine in this example) residue and one of them is a stop codon:

http://i-pv.org/gifs/stopCodon.gif

First you will have to generate such graphs. You will need to locally download and extract i-pv for this.You also need to locally install perl (I recommend strawberry perl for this) and circos since i-pv depends on them. The output opens within a browser. And you can use the output in your mobile device. If you have trouble generating such a plot for your gene, let me know, I will generate one for you.

I hope this helps,

Good luck with your research,

[harpreetmanku04]

it sounds difficult to do...i will try to do it... I did mean by above question is there any software where i enter sequence and it results into displaying stop codons???

[Martombo]

then you can try expasy translate tool: http://web.expasy.org/translate/

[Ibrahim Tanyalcin]

Apparently I misunderstood your question. I think Martombo's suggestion about expasy translate tool is great!