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HSSP-BLOSUM62 Value and WebLogo

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

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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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