ACP Haplotyper- Advanced (help)

ACP Haplotyper creates a visual haplotype that can be used to identify conserved and non-conserved chromosomal regions between any of the 48 rat strains characterized as part of the ACP project. For the selected chromosome and between the selected strains, the tool compares the allele size data for microsatellite markers on the selected genetic or RH map.

Get Acrobat!The output of this tool is an Adobe Acrobat PDF file which will be emailed to you so the Acrobat Reader software will be required to view the results. For more instructions on the tool, including sample ACP Haplotyper output, please see the ACP Haplotyper Help Page.

Select map and chromosome
Map to be used*
Only v7 genetic maps have LOD data
Chromosome*
Flanking Marker or Distance #1
Enter name/distance to specify
the top of the map region
Flanking Marker or Distance #2
Enter name/distance to specify
the bottom of the map region
 
Select Strains and Color Scheme
Strains to Display*
Multiple selections allowed,
select 1 or more strains you wish to view
Primary Strain & color scheme *  
Secondary Strain & color scheme  
Color Schemes *

Normal (Primary and option secondary strains colored)
bp difference from Primary size (multicolor scheme)
bp difference from Primary size (red, white & blue scheme)

  
 
 
Advanced options
Placement LOD Threshold
Use to exclude markers placed at a LOD lower than the threshold value
Basepair Range
Two Allele sizes are considered equal when their values are within the entered basepair range value.
Hide Size Data
Hides allele size data, showing the visual haplotype without all allele sizes shown.
Document Contents
Only displays the analysis statistics, not the visual haplotype data.
Order Strains by ...
Orders strains according to % allele size identity or homology, or alphabetically by strain name 		% Identity
% Homology
Strain Name (alphabetically)
 
Interstrain distance calculations
Calculate distance with sliding window
Window Size
Slide Increment
 
 
Output Options
Output Format
Email Address*
 
 
* indicates required fields


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