WEBLOGO PLUS

Sagar Gaikwad and Mohit Agrawal

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

Sequence Logo

Background - WebLogo

A UC – Berkley Project What is Sequence Logo Generates Sequence logos. Input from Manual/FASTA/CLUSTAL

format

Reference : http://weblogo.berkeley.edu/

WebLogo

 Different residues at the same position are scaled according to their frequency.

Where Rseq – 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 Smax – Maximum possible entropy Sobs – Entropy of observed symbol distribution

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

Applications

for displaying TFBS

Motif discovery

Sequence Scanning

Drawbacks of WebLogo

Correlations between different positions of the alignment

Not interactive

Hard to spot infrequent characters

What is Nested WebLogo

Transcription factor have positional dependency

What is positional dependency

Nesting of WebLogo’s based on positional dependencies

Example

AGTCTACC AGTCCACGATGCTACGTAGTTTCGATGCTAGGATGTAACT

AGTCTACC AGTCCACGATGCTACGTAGTTTCGATGCTAGGATGTAACT

Wild card: T.*Position Set 2,4

Heat Map

What is heat map

Advantages Improves Readability

UI Flow

Web-Logo Creator Web-logo Drawer

Fasta File Reader

Position Dependency Reader

Graphics Display

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*

References

Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [Full Text ]

Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100

www.weblogo.berkley.edu Efficient representation and P-value computation for high-

order Markov motifs Paulo G. S. da Fonseca1, Katia S. Guimarães1 and Marie-France Sagot2

Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics Authors : Jun Xie and Nak-Kyeong Kim