1. Introduction
Sequence logos are a graphical way of representing and visualizing biological information developed by Tom Schneider and Mike Stephens. Generally they supercede consensus sequences as more precise and useful ways of conveying data. We modified Alpro and Makelogo program from Tom Schenider's Delila pacakage to make web-based user friendly sequence logo program. The output of this program will be in .gif format but you can also retrieve pdf file.
2. Title
: Total two different tiles can be incorporated in Sequence Logo image. The coordinate indicates the first position of string and size is the size of characters.
3. Sequence Format
: Sequence format should be in FASTA format. However, if you use this program with consensus matrix result, your input would be pattern matrix and consensus format of sequence file.
3. Alphabet Option
: Prior Proababilities of nucleotide sequence. These are observed frequencies of the Genome from which DNA sequences come from. Information content is computed based on these numbers. For protein sequences or alphabet sequences, these numbers are set by the program.
4. Display Options
1) Capital Letters:
: Letter on sequence logo be capitalized with this option.
2) Letter Outlines:
: Make each character as outline.
3) Boxed Characters:
: Show a dashed box around each character.
4) Number Positions:
: Each stack is numbered.
5) Boxed Character Shrinking Factor:
: factor by which to shrink characters inside dashed box.
6) Show Y axis:
: Put bars before and after each line
5. Advanced Layout Options
1) Begining to Ending Positions in Entered Sequence:
: FROM to TO range to make the logo over
2) Lower left hand corner (x, y) (cm):
: Lower left hand corner of the logo (in cm)
3) Rotation on page (degree):
: Angle to rotate the graph
4) Width of character (cm):
: The width of the logo characters, in cm
5) Height of vertical bars (cm):
: Height of vertical bar, in cm
6) Width of vertical bars (cm)
: Width of vertical bar, in cm
7) Height of vertical bars (bits)
: Height of the vertical bar, in bits
8) Number of character per Line
: Number of character stacks per line output.
9) Number of Lines
: Number of lines per page output
10) Inter-line seperation (cm)
: Line separation relative to the barheight