identify where is the starting point for the synthesis of a protein in the DNA

For indentify a starting point in RNA or DNA my function search all ATG or M in the sequece and report the linear position of start, than the function search TAA and TAG for stop codon and report the end position.

For the end codon what I have to search? only TAA and TAG or TGA and TGG too?

How is possible some protein begin with "F" as in "FFRE..." and not "M..." ?

Than it result more starting point solutions respect to protein found in GeoBank, what are the add restriction for limit that number?

Are there easy to search sequences that make sure that is a start of the protein code? as seems to me "AGG AGG" but is not clear where they should be in the array and not seems general seen proteins.

Can the synthesis of protein be affected by temperature? What other factors come into play?

Passing my function to DNA of one virus, the first test, the function identifies in the end of virus many little proteins of 2 3 4 5 10 protein letters. These little protein pieces are really sintetized? or there is a min lenght for sintetized proteins?

  • 1
    $\begingroup$ This seems like a homework question. If you want a software to identify ORFs for another project, @PPK's answer is a good way to start. If you need to make a function to do so as part of a project for a subject, you should look for all stop codons as possibilities. $\endgroup$ – csgroen Jul 30 '20 at 11:18

You seem to be interested in identifying potenital coding regions in a DNA sequence. These regions are called open reading frames (ORF) because they are open to translation.
As detailed in the linked Wikipedia article, an ORF usually starts with an ATG and ends with one of the stop codons (TAA, TGA or TAG in DNA space). However, there are many ORFs that are not translated at all, particularly short ones.

Since finding ORFs is an old and established task in bioinformatics there are many algorithms availabe to do this. I would suggest using such an existing tool because they often have additional features and bugfixes. There is a list in the link above.

Estimating the stability and likelihood of a particular amino acid sequence is much more complicated. There are many tools for protein structure prediction that may be worth having a look at.


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