Module Detail Information

Name:Dottup
Type: Module
Short URL:
http://bit.ly/1B7EckI
Description:A dotplot is a graphical representation of the regions of similarity between two sequences. The two sequences are placed on the axes of a rectangular image and (in the simplest forms of dotplot) wherever there is a similarity between the sequences a dot is placed on the image. Where the two sequences have substantial regions of similarity, many dots align to form diagonal lines. It is therefore possible to see at a glance where there are local regions of similarity as these will have long diagonal lines. It is also easy to see other features such as repeats (which form parallel diagonal lines), and insertions or deletions (which form breaks or discontinuities in the diagonal lines). dottup looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of these words. This is a fast, but not especially sensitive way of creating dotplots. It is an acceptable method for displaying regions of substantial similarity between two sequences. Using a longer word (tuple) size displays less random noise, runs extremely quickly, but is less sensitive. Shorter word sizes are more sensitive to shorter or fragmentary regions of similarity, but also display more random points of similarity (noise) and runs slower.
Executable:
/dottup
Input Parameters:
 - A Sequence
 - B Sequence
 - A Start
 - A End
 - A Reverse
 - A Ask
 - A Nucleotide
 - A Protein
 - A Lower Case
 - A Upper Case
 - A Format
 - A Database Name
 - A Entry Name
 - A UFO Features
 - A Features Format
 - A Features File
 - B Start
 - B End
 - B Reverse
 - B Ask
 - B Nucleotide
 - B Protein
 - B Lower Case
 - B Upper Case
 - B Format
 - B Database Name
 - B Entry Name
 - B UFO Features
 - B Features Format
 - B Features File
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Word Size
 - Graph Prompting
 - Graph Description
 - Graph Title
 - Graph Subtitle
 - Graph X-Axis Title
 - Graph Y-Axis Title
 - Graph Output Directory
 - Graph Type
 - Version
 - No Box
 - Stretch
Output Parameters:
 - Graph Output File
File size:32.27 KB
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