GENIO/logo
RNA/DNA & Amino Acid Sequence Logos
 It is helpful for improvements and further development to receive feedback about GENIO/logo sequence logo program. You are welcome to send comments, suggestions and bug reports to Niels Mache (mache at struktur dot de). If you find GENIO/logo service useful please register. Registered users may receive email about enhancements and changes in GENIO/logo.
Step 1: Input nucleotide or amino acid sequences in FASTA file format
You may input your sequences by cut-and-paste into the sequence window below or (easier) enter a filename and upload a sequence file. The sequence given must contain at least two (aligned) sequences. Input sequences are in FASTA format. In FASTA format, the sequences are separated by a single line started with the ">" sign and followed by an optional comment string. Don't forget to set the type of your sequence (nucleotide or amino acid).
 
Sequence window (cut-and-paste). DNA or amino acid sequence, one-letter code, upper/lower case, spaces/invalid letter ignored:

 
Sequence file (use Netscape Version >= 2.0):

 or load demonstration file (173 Homo Sapiens PolyA sites): 
 
 
 The sequence is a      Nucleotide sequence 
    Amino acid sequence 
 
Step 2: Sequence logo type 
Set the sequence logo type. Optionally apply letter replacement and nucleotide/amino acid coloring rules. Replacement rules are useful for amino acid sequences to group amino acids into groups with similar physical/chemical properties.  For each letter a color, given as a RGB value, can be defined. See Example below.
 
 
 a priori nucleotide/amino acid distribution    equally distributed letter frequency
  measure letter distribution of complete sequence 
 calculate information content of nucleotide/amino acid word 
 frequencies rather then single nucleotides/amino acids
 word length (1..4)  
 letter replacement rules    apply replacement rules below 
 sequence case sensitivity    ignore character case of sequence symbols, convert to uppercase 
 
Letter replacement and coloring rules:

 
 
Step 3: Sequence logo drawing options 
 Set the drawing options below.
 
 sequence logo title   draw title  (default is sequence filename)
  no title
 position numbering start numbering with position number 
  skip position number '0' when numbering positions 
 background lines   background lines on
  background lines off
 page numbering   page numbering on
  page numbering off
 threshold for drawing 
 sequence letters
  minimum threshold
 
Step 4: Submit data 
 
 
 
Step 5: View sequence logo and download Postscript/EPS and GIF file 
A new window appears showing the sequence logo. Be patient, it may take a moment.
 



Problems, suggestions, remarks? Send email to
Niels Mache (mache at struktur dot de)  My home page is here.