RNA/DNA & Amino Acid Sequence Logos
Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. We developed the program GENIO/logo for the calculation and display of positional dependent information content of nucleotide and amino acid sequences. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors. The graphs given below show the positional information content of splice sites of human split genes, translation initiation and PolyA site (DNA sequences from GENIO/seq database) .
|Schneider T.D. and Stephens R.M.
"Sequence logos: a new way to display consensus sequences."
Nucleic Acids Res., 18(20):6097-6100, 1990.
Download the paper here (Postscript file).
|Claude E. Shannon and Warren Weaver
"The Mathematical Theory of Communication" University of Illinois Press, Urbana, 1949.
|On-line references, software:
Tom Schneider's delila package.
Tom Schneider's Hompage.
Steven E. Brenner's WebLogo
J. Gorodkin et al., RNA Structure Logos
Thomas D. Schneider, Garry D. Stormo, Larry Gold and Andrzej Ehrenfeucht
"Information Content of Binding Sites on Nucleotide Sequences", J. Mol. Biol. (1986) 188, 415-431
|GENIO/logo||via http connection|
|GENIO/logo||via secure connection, SSL (Secure Socket Layer)|
|GENIO/seq||- A Non-Redundant Eukaryotic Gene Database of Annotated Sites and Sequences|
|GENIO/scan||- EST/STS Guided Identification of Genes in Human Genomic DNA|
|GENIO/cover||- GENIO/scan EST Coverage Analysis of Currently Known Eukaryotic Coding Sequences|
|GENIO/logo||- Nucleic and Amino Acid Sequence Logos|
|GENIO/splice||- Splice Site and Exon Prediction in Human Genomic DNA|
|GENIO/frame||- Frame Shift Analysis and Sequencing Error Detection|
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