Sequence motifs, information content, logos, and HMM’s. Morten Nielsen, CBS, BioCentrum, DTU. Outline. Multiple alignments and sequence motifs Weight matrices and consensus sequence Sequence weighting Low (pseudo) counts Information content Sequence logos Mutual information

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Evolution of Amino Acid Frequencies in Proteins. Inferred Order of Introduction of Amino Acids into the Genetic Code. Extant Genetic Code. From: http://www.millerandlevine.com/Code-Table-Rect.html. Is not a “frozen accident” There must have been earlier version

Frequencies. Y axis, X axis. Y Axis—typically shows frequencies. Hint: think “Y on the left, X on the bottom…” OR Remember this? Y = f(X). X Axis—typically shows values/value categories. Bar Graph—Nominal Level Measure. Frequency. Frequency Polygon—Interval or Ratio Level of Measures.

FREQUENCIES. Running the Analysis. The Frequencies procedure provides statistics and graphical displays that are useful for describing many types of variables. The Frequencies procedure is a good place to start looking at your data.

Relative Frequencies. and Pie Charts. Relative frequency of . 1. Sweet (fraction). 2. Sour (decimal). 3. Bland (%). 4. Pie Chart angle for Sour. 540 trains were surveyed. 5. How many were right on time?. Early. Late. 120 0. 100 0. Right on time. 80. Relative frequency of . 20 / 80.

Use of 4 km, 1 hr, Precipitation Forecasts to Drive a Statistical-Distributed Hydrologic Model for Flash Flood Prediction J8.4 20 th Conference on Hydrology, AMS Annual Meeting 2006 Seann Reed 1 , Richard Fulton 1 , Ziya Zhang 1,2 , Shucai Guan 1,3 Presented by John Schaake 4

Beat Frequencies. Assume two waves are superpositioned Amplitudes are the same Frequencies & wavelengths are different Use fact that. to yield. Groups and phases. Cosine portion defines “envelope” within which sine portion oscillates Envelope moves with a speed.

Identifying Frequencies. Terms:. Loudness Pitch Timbre. Loudness. Sound loudness is a subjective term describing the strength of the ear's perception of a sound.

Spatial Frequencies . Why are Spatial Frequencies important?. Efficient data representation Provides a means for modeling and removing noise Physical processes are often best described in “frequency domain” Provides a powerful means of image analysis. What is spatial frequency?.

Radio Frequencies. Oscillator. Feedback loop. Oscillator. As the output of the amplifier is fed to the input, feedback or oscillation occurs. Tuned Oscillator. Oscillator. When properly tuned to a high enough frequency, the oscillator will produced radio frequencies