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HSSP-BLOSUM62 Value and WebLogo

In this presentation, Dr. Bernard Chen from the University of Central Arkansas offers an in-depth overview of HSSP-BLOSUM62 values and their application in protein logos using WebLogo. The discussion includes how to interpret protein logos, the significance of amino acid frequency, and methods to generate logos effectively. Key insights into structural similarity, hydrophobicity values, and specific amino acid occurrences provide a framework for analyzing protein motifs. Attendees will learn practical steps for using WebLogo to visualize protein sequence data.

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HSSP-BLOSUM62 Value and WebLogo

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  1. HSSP-BLOSUM62 Value and WebLogo Dr. Bernard Chen Ph.D. Assistant Professor Department of Computer Science University of Central Arkansas Fall 2009

  2. Outline • WebLOGO • HSSP-BLOSUM62 Value

  3. Protein Logo

  4. Protein Logo • The upper box gives the number of members belonging to this motif, the secondary structural similarity and the average HSSP-BLOSUM62 value. • The graph demonstrates the type of amino acid frequently appearing in the given position by amino acid logo. It only shows the amino acid appearing with a frequency higher than 8%. The height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. • The x-axis label indicates the representative secondary structure (S), the HSSP-BLOSUM62 measure (H-B) and the hydrophobicity value (Hyd.) of the position. The hydrophobicity value is calculated from the summation of the frequencies of occurrence of Leu, Pro, Met, Trp, Ala, Val, Phe, and Ile.

  5. Some Extensions

  6. How to Generate it • 1. go to http://weblogo.berkeley.edu/ • 2. select “Create” • 3. generate protein information • 4. change setting: • Logo Size per Line: 30 * 30 • Color Scheme: Custom (See Below.) • Black: AVLIPFMW • Red: DE • Blue: RHK • Green: GCSTY • Purple: QN • White (ffffff): . • 5. Modify the graph a little bit

  7. Generate Motif information • We only care the amino acid appearing with a frequency higher than 8%. • For example: (amino_acid sequence = 'V','L','I','M','F','W','Y','G','A','P','S','T','C','H','R','K','Q','E','N','D') input_value=“ 3 3 2 1 1 0 2 12 13 7 10 7 1 2 4 4 3 5 5 5 4 4 2 1 3 1 3 8 13 7 10 7 1 1 4 4 4 4 5 5 4 4 2 1 2 1 2 9 14 8 10 7 1 2 4 4 4 4 5 5 3 3 1 0 2 0 2 11 12 7 10 7 1 1 4 4 4 5 5 7 4 4 2 1 2 1 2 9 13 7 9 7 1 1 4 4 4 5 5 6 4 4 2 0 2 1 3 9 11 7 9 7 1 2 4 4 4 6 5 6 4 4 2 1 2 1 3 10 11 7 8 7 1 1 4 4 4 5 5 6 4 5 2 1 3 1 3 9 12 7 8 7 1 1 4 4 4 5 4 6 5 4 2 1 3 1 3 9 12 7 8 7 1 1 5 4 3 5 4 6 "

  8. Generate Motif information • The code and file: • Code: motif_logo_pure.py (written in Python) • Motif logo file: motif_logo.txt

  9. Outline • WebLOGO • HSSP-BLOSUM62 Value

  10. BLOSUM62 Matrix

  11. HSSP-BLOSUM62 Measure Example • HSSP-BLOSUM62 Value= =

  12. HSSP-BLOSUM62 Measure

  13. HSSP-BLOSUM62 Code • Code: HB value file version • Input example: super_rule_value.txt

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