1. WEBLOGO PLUS Sagar Gaikwad and Mohit Agrawal

2. LTMT.-RGDIGNYLGLTVETISRLLGRFQKLGVL LTMT.-RGDIGNYLGLTVETISR----------- LTMT.-RGDIGNYLGLTVETISRLLGRFQKLGVI LTMT.-RGDIGNYLGLTVETISRLLGRFQKSGLI LTMT.-RGDIGNYLGLTVETISRLLGRFQKSGML LTMT.-RGDIGNYLGLTIETISRLLGRFQKSGMI LTMT.-RGDIGNYLGLTVETISRLL LPLT.-RADISDFLGLTNETVSRQLTRLRADGVI LPLT.-RADIADFLGLTIETVSRQLTRLRTDGLI LPLS.-RAEIADFLGLTIETVSRKLTKLRKSGVI LPLS.-RAEIADFLGLTIETVSRQLTRLRKEGVI LPLS.-RAEIADFLGLTIETVSRQMTRLRKWGVI LPLS.-RAEIADFLGLTIETVSRQMTRLRKSGVI LPLS.-RAEIADFLGLTIETVSRQMTRLRKIGVI

3. Sequence Logo

4. Background - WebLogo  A UC – Berkley Project  What is Sequence Logo  Generates Sequence logos.  Input from Manual/FASTA/CLUSTAL format Reference : http://weblogo.berkeley.edu/http://weblogo.berkeley.edu/

5. WebLogo  Different residues at the same position are scaled according to their frequency.  Where R seq – sequence conservation at a particular position in alignment  n – Symbol (like A G T C for DNA)  N – number of distinct symbols. 4 for DNA /RNA – 20 for Protein sequences  S max – Maximum possible entropy  S obs – Entropy of observed symbol distribution

6. Advantages  can rapidly reveal significant features of the alignment otherwise difficult to perceive  Interpret the sequence-specific binding of the protein CAP to its DNA recognition site  Works for DNA/RNA/Protein logos  can illuminate patterns of amino acid conservation that are often of structural or functional importance  Open source

8. Applications  for displaying TFBS  Motif discovery  Sequence Scanning

9. Drawbacks of WebLogo  Correlations between different positions of the alignment  Not interactive  Hard to spot infrequent characters

10. What is Nested WebLogo  Transcription factor have positional dependency  What is positional dependency  Nesting of WebLogo’s based on positional dependencies

11. Example AGTCTACC AGTCCACG ATGCTACG TAGTTTCG ATGCTAGG ATGTAACT AGTCTACC AGTCCACG ATGCTACG TAGTTTCG ATGCTAGG ATGTAACT Wild card: T.* Position Set 2,4

12. Heat Map  What is heat map Advantages  Improves Readability

13. UI Flow Web-Logo Creator Web-logo Drawer Fasta File Reader Position Dependency Reader Graphics Display

14. Out contribution  No open source java implementation available for WebLogo  Implementation of graphical display of web logo in Java  Interactive – Zoom in and Zoom out feature for clear visibility  Heat Maps  Nested Logos  3D Heat Maps*

15. References  Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [Full Text ] Crooks GEHon GChandonia JMBrenner SEFull Text  Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100Sequence Logos: A New Way to Display Consensus Sequences.  www.weblogo.berkley.edu www.weblogo.berkley.edu  Efficient representation and P-value computation for high-order Markov motifs Paulo G. S. da Fonseca 1, Katia S. Guimarães 1 and Marie-France Sagot 2Paulo G. S. da Fonseca 1Katia S. Guimarães 1Marie-France Sagot 2  Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics Authors : Jun Xie and Nak-Kyeong Kim