If RNA or DNA sequences, e.g. metagenome of a sample are given, is there a software or technology allows us to construct/translate "pseudo-proteins" from these sequences? If so, would you mind describing also the key steps?
If the above is possible, is there then any software/technology to predict protein-protein or protein-DNA/RNA interactions given either the protein sequence or DNA sequences are available?
Thank you in advance!
It is a standard procedure to translate DNA or RNA open reading frames into protein sequences. Either the nucleic acid sequence or the protein sequence can be compared to all known sequences using a tool such as BLAST to identify homologous proteins that are likely to have a similar function.
Hi Adam - Thanks for the response. Though, wouldn't it take quite a long time to do so if the sequence is very large?
Do you also know if there is a way to predict protein-protein interactions (I guess instead of doing crystal structure)? In other word, can we predict the tertiary/quaternary structure of a protein given its DNA/RNA sequences?
Thank you so much!
Predicting structure from the sequence of a protein is not something that can be easily done. There are people working on structure modeling but each protein require a lot of computational power and expertise, and the results are of varying quality. The best you can do is to look if you are able to identify sequence similarity to known functional domains,which can give you some indication of possible interactions and functions.
Even if you had a structure that will not give you information about actual interactions, for that you will have to preform IP followed by mass spectrometry.
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