For example:
A DNA sequence is translated into the sequence:
N-MKTSTRFLDGYFPVAANK-C
-Mutation-
Which leads to the production of:
N-(Met)KNAAVPFYGDLFRTSTKM-C
The obvious problem is that an inversion will invert the codon sequences (ex. CUU GGA-> AGG UUC = LG-> RF). Is there any known mechanism in nature through it is possible to change something like "AAU UCU GAC" into "GAC UCU AAU"?
I cannot think of any way for this to occur - but it would be straightforward to test whether this mechanism exists (or existed in the very ancient past, before translation as we know it today came to exist). I've been running blast searches using inverted amino acid sequences of arbitrarily chosen proteins to see if I find any interesting matches, but haven't gotten any expect values lower than 1x10^-3. I've been doing this manually because I am not trained in bioinformatics - do any of you know where I could learn enough to make a program that will automatically go through inverted amino acid sequence blast searches and retrieve the matches with low expect values?
Thanks!
You are both right, but as Maximilian Paradiz wrote in his original question, simple inversion of NA sequence will NOT lead to inversed peptide sequence. I doubt there would be any simple mechanism for that. And it would be quite useless, because inversed protein will not have "inversed properties", it would be something completely different and unrelated.
The question is, Maximilian, how long inversed peptides you want. Of course for short sequences you will find something just by chance, but the probability decreases with every additional amino acid.
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