Module Detail Information

Name:CpG Plot
Type: Module
Short URL:
http://bit.ly/1B7EfwZ
Description:cpgplot identifies CpG islands in one or more nucleotide sequences. The ratio of observered to expected number of GC dinucleotides patterns is calculated over a window (sequence region) which is moved along the sequence. The calculated ratios are plotted graphically, together with the regions which match this program's definition of a "CpG island" (a CG dinucleotide rich area). A report file is written giving the input sequence name, CpG island parameters and data on any CpG islands that are found. The ratio of observered to expected number of GC dinucleotides patterns is calculated over a window of user-specified size (-window parameter). The window is slid along the sequence and the ratio recalculated until the end of the sequence is reached. By default, cpgplot defines a CpG island as a region where, over an average of 10 windows and not less than 200 bases, the calculated (%G + %C) content is over 50% and the calculated Observed/Expected ratio is over 0.6. These conditions can be modified by setting the values of the appropriate parameters. The Observed number of CpG patterns in a window is simply the number of times a 'C' is found followed immediately by a 'G'. The Expected number of CpG patterns is calculated for each window as the number of CpG dinucleotides you would expect to see in that window based on the frequency of C's and G's in that window. Thus, the Expected frequency of CpG's in a window is calculated as the number of 'C's in the window multiplied by the number of 'G's in the window, divided by the window length. Expected = (number of C's * number of G's) / window length
Executable:
/chaos
Input Parameters:
 - Sequence
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Graph Type
 - Graph Prompting
 - Graph Description
 - Graph Title
 - Graph Subtitle
 - Graph X-Axis Title
 - Graph Y-Axis Title
 - No Plot
 - Version
 - Window Size
 - Minimum Length
 - Minimum Observed to Expected Ratio
 - Minimum Percentage
 - Output Feature Format
 - Output Features Filename
 - Output Features Extension
 - Output Features Directory
 - Output Features Base Filename
 - Output Features Seperate Files
 - Don't Display Obs:Exp
 - Don't Display CpG Islands
 - Don't Display Percent C + G
Output Parameters:
 - Output File
 - Graph Output File
 - Graph Output Directory
 - Output Directory
 - Output Features File
File size:34.51 KB
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