TY - JOUR
T1 - Displaying the information contents of structural rna alignments
T2 - The structure logos
AU - Gorodkin, J.
AU - Heyer, L. J.
AU - Brunak, S.
AU - Stormo, G. D.
N1 - Funding Information:
This work was partially supported by NIH grant HG00249 to G.D.S. J.G. and S.B. were supported by the Danish National Research Foundation. We thank Russ Altman and Sean Eddy for useful comments and suggestions.
PY - 1997
Y1 - 1997
N2 - Motivation: We extend the standard ‘Sequence Logo’method of Schneider and Stevens (Nucleic Acids Res., 18, 6097–6100, 1990) to incorporate prior frequencies on the bases, allow ft, r gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Results: Given an alignment of RNA sequences with the base pairings indicated, the program will calculate the information at each position. including the mutual information of the base pairs. and display the results in a ‘Structure Logo’. Alignments without base pairing can also be displayed in a ‘Sequence Logo’. but still allowing gaps and incorporating prior frequencies if desired. Availability: The code is available from, and an Internet server can be used to run the program at, http://www.cbs.dtu.dklgorodkin/appl/slogo.html. Contact: E-mail: [email protected].
AB - Motivation: We extend the standard ‘Sequence Logo’method of Schneider and Stevens (Nucleic Acids Res., 18, 6097–6100, 1990) to incorporate prior frequencies on the bases, allow ft, r gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Results: Given an alignment of RNA sequences with the base pairings indicated, the program will calculate the information at each position. including the mutual information of the base pairs. and display the results in a ‘Structure Logo’. Alignments without base pairing can also be displayed in a ‘Sequence Logo’. but still allowing gaps and incorporating prior frequencies if desired. Availability: The code is available from, and an Internet server can be used to run the program at, http://www.cbs.dtu.dklgorodkin/appl/slogo.html. Contact: E-mail: [email protected].
UR - http://www.scopus.com/inward/record.url?scp=0031473030&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/13.6.583
DO - 10.1093/bioinformatics/13.6.583
M3 - Article
C2 - 9475985
AN - SCOPUS:0031473030
SN - 1367-4803
VL - 13
SP - 583
EP - 586
JO - Bioinformatics
JF - Bioinformatics
IS - 6
ER -