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mRNA Site Predictor
Example
Output
List of Outputs
Tools
Sites in User Submitted Sequence
Sites in Known Genes
Check Results
Documentation
Output Format
Overview Plot
Top Sites
Full Site Detail
DSM/HMM Used
DSM Overview Plot
Element Positions
Nucleotide Frequency
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Each site in the list above is also explored in detail in
the output. The highest scoring site for CYC1 is shown
below as an example. The upper left pane of the table contains
the position, DSM, e-value, and sequence at the putative processing
site. The upper right contains a plot that shows an expanded
plot of the DSM analysis of the sequence surrounding the putative
plot. Five separate plots are shown, corresponding to the relative
likelihoods of the four hexamer elements and the processing
site: Blue: Element #1, Green:
Element #2, Magenta: Element #3, Red: Processing Site,
Gray: Element #4.
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The four lower panels list up to four (cut off at DSM=3) most likely sites for each of the four control elements in the DSM. For each listed putative element, the information given is sequence position, sequence, DSM, and the independent log-likelihood. The independent log-likelihood is the base 10 logarithm of the ratio of the probability of the hexamer being generated by the element model to the probability of the hexamer being generated by random yeast sequence. In contrast the DSM value gives the relative likelihood of the hexamer being used as the element within the context of the complete DSM. Comparison of the DSM and the independent log-likelihood allows investigation of the use of sub-optimal words as processing elements.