Main principles of MatrixSS program
The program MatrixSS is designed for searching in genome sequences for the regions with potentially significant secondary structure (SS). It is assumed that SS is determined by the structure of RNA that could be translated from this region.
The MatrixSS program is based on two principles:
As follows from the principle 2, for the structural RNA the E-score value, like mononucleotide content, varies a little. The program MatrixSS applies this property for determining the regions with nucleotide content preferable for formation of functionally significant SS. If the E-score value in some genome DNA region is less than some threshold value
average(E-scorestruct) - standard_deviation(E-scorestruct)
or it exceeds the threshold value
average(E-scorestruct) + standard_deviation(E-scorestruct),
then the program MatrixSS considers this region as lacking potential SS. Here
Note that too large E-score value also evidences about the fact that the sequence analysed is not referred to the class of structural RNA. However, this does not mean that this sequence is enable to form SS. On the contrary, in this case, the potential SS would be too much stable for performing any functions (this viewpoint is supported by 2 statements: (1) very stable SS is formed very slowly; (2) the form of very stable SS is very susceptible to mutations, hence it is not selected in course of evolution). The exception is 5'UTR sequences in eukaryotes. It is known that highly stable SS of 5'UTR RNA is capable to inhibit its translation, that is, this high stability is of biological significance. However, this function is independent from the form of SS, but the energy (stability) of SS is significant. Taking this into account, eukaryotic mRNAs (in particular, their 5'UTR regions) can not be referred to the class of structural RNA.