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i am looking for likely truncation sites to prove recombination in sequences. i have 4 sequences. i believe one to be the "real sequence" and the other 3 to be recombinants caused by cleavage possibly due to Arg c proteinase. I know my sequences overlap due to multiple alignments i have performed using UniProt and i have chosen the enzyme due to carrying out cuts on Expasy cutter. If anyone could point me in the right direction this would be much appreciated. many thanks in advance

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-1 question not currently legible and not clear what you are struggling with. edit the question to make it readable and make the question itself clearer. –  GriffinEvo Dec 16 '13 at 16:35
    
thank you i have rephrased the question, i am new to this site i am looking for truncation sites in sequences if you have any information on useful literature it would be greatly appreciated.many thanks –  user5182 Dec 16 '13 at 17:11
    
Can you please make this a redable post? Posting a ton of sequences seems not helpful to me at leat unless you re-phrase your question. These are protein sequences, so you will not find any stop codons. –  Chris Dec 16 '13 at 17:20
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using the "preformatted text" option on the alignment text would help to make it much more readable. And RE your comment on you other post - I am being helpful so there is no need for rude comments, properly written and clear questions get better answers, this is how things are done on the SE sites. –  GriffinEvo Dec 16 '13 at 17:40
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thank you with regards to the pre formatted text option, and it was not a rude comment i am new to the website and everyone has been extremely helpful however if you read the post you would see it is not a duplicate question and an unnecessary response since i am new and trying to navigate my way around the site. many thanks –  user5182 Dec 16 '13 at 17:44
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closed as unclear what you're asking by MattDMo, GriffinEvo, biogirl, kmm Dec 16 '13 at 18:10

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question.If this question can be reworded to fit the rules in the help center, please edit the question.

1 Answer

The sequences you have posted seem to be (protein) amino acid sequences. The stop codon are present in DNA sequences and in mRNA sequences.

In DNA, the bases are A, G, C and T; stop codons are TAG, TGA and TAA. In RNA, the bases are A, G, C and U; stop codons are UAG, UGA and UAA. In DNA and RNA, other letters are used to specify degeneracy.

What you have here looks like protein sequences. So, there are no stop codons in sequences you have posted.

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thank you this is correct i meant to say i was looking for truncation sites not stop codons. –  user5182 Dec 16 '13 at 17:10
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