RNALogo - a new approach to display structural RNA alignment


Home CreateLogo Gallery Documentation Help

Features of RNALogo
Compared with other tools
System flow of RNALogo
References


► Features of RNALogo:

 RNALogo concentrate the following information contents into a single graph :
   The RNA secondary structure 
 
The general consensus of the sequences

  
The order of predominance of the residue at every position
  
The relative frequencies of every residue at every position
  
The amount of information present at every position in the sequence
  
The perfectly/highly/low conserved base pairs in the structure
  
The perfectly conserved nucleotide in the sequences
  
The mutual information at the base-paired positions

 

 Other features:
  
Accept 4 different kinds of input format and provide 5 different kinds of output format
  
Accept input RNA sequences without alignment or structure
  
Provide JavaScript displaying functions in SVG format
     - raw value pop-up when the cursor moves on nucleotide, mutual information, and pairing ratio
     - different view of RNALogo by clicking on SVG graph
   Provide the pseudoknot annotation
   Provide frequency plot view, custom logo settings and etc


► Compared with other tools :

Comparing features

RNALogo

sequence logo

structure logos

enoLOGOS

CorreLogo

Display with RNA 2D structure

Yes

-

-

-

-

Display mutual information

Yes

-

Yes

Yes

Yes

Support frequency ploy drawing

Yes

Yes

-

-

-

Support pseudoknot annotation

Yes

-

-

-

-

Accept various input formats

Yes

-

-

Yes

-

Accept input unaligned sequences Yes - - - -
Visualization of alternative interaction

-

-

- Yes Yes
Visualization / cutoff by standard deviation

-

- - -

Yes

Small sample error correction taken into account

-

-

-

-

Yes



► System flow of RNALogo :


► References :

Displaying the information contents of structural RNA alignments: the structure logos. J. Gorodkin, L.J. Heyer, S. Brunak and G.D Stormo. Computer Applications in the Biosciences (CABIOS) 13:583-586 (1997).

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. Eckart Bindewald, Thomas D. Schneider and Bruce A. Shapiro, Nucleic Acids Research 34:W405-W411 (2006).

enoLOGOS: a versatile web tool for energy normalized sequence logos. Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo5 and Panayiotis V. Benos. Nucleic Acids Research 33:W389-W392 (2005).

Sequence logos: a new way to display consensus sequences. Thomas D.Schneider and R.Michael Stephens. Nucleic Acids Research 18:6097-6100 (1990).

WebLogo: A Sequence Logo Generator. Gavin E. Crooks, Gary Hon, John-Marc Chandonia, and Steven E. Brenner. Genome Research 14:1188-1190 (2004).


Department of Computer Science and Information Engineering, National Central University, Tao-yuan, Taiwan
Contact with site administrator:
Tzu-Hao Chang