weblogo plus
DESCRIPTION
WebLogo Plus. Sagar Gaikwad and Mohit Agrawal. LTMT.-RGDIGNYLGLTVETISRLLGRFQKLGVL LTMT.-RGDIGNYLGLTVETISR----------- LTMT.-RGDIGNYLGLTVETISR----------- LTMT.-RGDIGNYLGLTVETISR----------- LTMT.-RGDIGNYLGLTVETISR----------- LTMT.-RGDIGNYLGLTVETISRLLGRFQKLGVI - PowerPoint PPT PresentationTRANSCRIPT
• 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
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
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
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