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WEBLOGO PLUS
Sagar Gaikwad and Mohit Agrawal
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• 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
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Sequence Logo
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Background - WebLogo
A UC – Berkley Project What is Sequence Logo Generates Sequence logos. Input from Manual/FASTA/CLUSTAL
format
Reference : http://weblogo.berkeley.edu/
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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
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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
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Applications
for displaying TFBS
Motif discovery
Sequence Scanning
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Drawbacks of WebLogo
Correlations between different positions of the alignment
Not interactive
Hard to spot infrequent characters
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What is Nested WebLogo
Transcription factor have positional dependency
What is positional dependency
Nesting of WebLogo’s based on positional dependencies
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Example
AGTCTACC AGTCCACGATGCTACGTAGTTTCGATGCTAGGATGTAACT
AGTCTACC AGTCCACGATGCTACGTAGTTTCGATGCTAGGATGTAACT
Wild card: T.*Position Set 2,4
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Heat Map
What is heat map
Advantages Improves Readability
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UI Flow
Web-Logo Creator Web-logo Drawer
Fasta File Reader
Position Dependency Reader
Graphics Display
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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*
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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