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ACP Haplotyper Help
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RGD Definition

"This tool allows visualization of chromosomal segments that are conserved between different inbred strains and also provides a measurement of relatedness between these inbred strains. Results are presented as PDF documents containing the interstrain identity matrices and a visual haplotype showing conserved microsatellite marker allele sizes across the selected chromosome. It uses the Allele Characterization Project dataset in combination with various genetic and Radiation Hybrid maps (also see RH Map Server)."

 

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Visualizing interstrain conservation using ACP Haplotyper

ACP Haplotyper provides a way to visualize genomic regions that are conserved between various inbred strains. Two versions of the tool are provide, a Simple and Advanced version. The algorithms used are the same, however, the Advanced version provides more options for customizing the display and the ability to change certain parameters for the calculations.

Using the Simple form, follow these steps to use ACP Haplotyper:

  1. Select a map upon which to base the analysis. Typically the Radiation Hybrid map is the best option as it has the most markers mapped on it and will provide the most information unless specific markers of interest to you are not present on the RH.
  2. Select the chromosome you wish to analyze.
  3. Select the strains you wish to compare (from 1 to all 48)
  4. Select a Primary Strain - this is the reference strain against which the other strains are compared for the purposes of the visualization. Select a color for this strain's data on the visual haplotype (only relevant if using the "Normal" color scheme option)
    [NB: the Common Alleles option represents an artificial strain created by using the most common allele size for each marker, it can be useful as an indication of the makeup of the 'average' strain}
  5. [Optional] Select a secondary strain and color. This is useful if you are looking at a particular cross and wish to see how the two strains compare with respect to each other (and other strains).
  6. Select a color scheme to use. The Normal color scheme is best for comparing two strains to each other (and to the rest of the selected strains), the Multicolor and Red/White/Blue color schems are two alternative ways of seeing a more global picture of allele conservation across the selected strains.
  7. Enter your email address and click 'Display Haplotypes'

The results will be emailed to you within a few minutes, for more information on the results and to see sample output, see the ACP Haplotyper Results section below.

Below is a more detailed explanation of each element of the Advanced ACP Haplotyper form.

RGD: ACP Haplotyper Help

Advanced ACP Haplotyper Help

Map to be used

Chose one of the available genetic or radiation hybrid maps. This map is then used to provide the map order of the microsatellite markers used to create the ACP haplotype image.

Chromosome

Select the chromosome that you would like to view the ACP haplotype for.

 

Flanking marker or Distance #1

Can be used to limit the region of the chromosome that is analyzed. Enter the first flanking marker or map location (cM or cR as appopriate) that defines the start of the region to be displayed. Normally one would also enter a second flanking marker or distance, however, if the second value is left empty the tool will analyze the region from the first marker to the end of the chromosome.

 

Flanking marker or Distance #2

Can be used to limit the region of the chromosome that is analyzed. Enter the second flanking marker or map location (cM or cR as appopriate) that defines the end of the region to be displayed. Normally one would also enter a starting flanking marker or distance, however, if the start value is left empty the tool will analyze the region from the start of the chromosome to the second marker.

 

Strains to Display

Select one or more individual rat strains to be included in the analysis. Chose 'All 48 Strains' to include all possible strains.

 

Primary Strain and Color Scheme

Select one primary strain against which all other selected strains are compared. This choice affects the output in different ways depending on the color scheme selected.

 

Secondary Strain and Color Scheme

This is an optional selection - select one secondary strain against which all other selected strains are compared to . This choice affects the output in different ways depending on the color scheme selected:

 

Color Schemes

The color schemes affect how the visual haplotypes are colored and are best suited to different types of analysis:

Color Scheme Best Used for Description
Normal Comparing two strains against each other For each marker, if the allele size in Strain A matches that of the primary strain, the marker block is colored according to the primary strain color. If the Strain A size is different from the primary strain but the same size as that found in the secondary strain (if selected) then the block has the secondary color. If the size matches neither primary or secondary strains it is colored black. If there is no allele size data for a marker in a particular strain this is indicated by a 'X'.
Multicolor Scheme Comparing many strains to see discontinuous haplotypes spread across the chromosome. Blocks for each marker are colored according to the size difference between the allele size in the particular strain and the size of the Primary Strain. Blocks are colored according to a discontinuous color scheme depending on the base pair size of the marker allele in a given strain as compared to that marker's allele size in the primary strain.
Red, White and Blue Comparing many strains to see overall patterns of conservation Blocks for each marker are colored according to the size difference between the allele size in the particular strain and the size of the Primary Strain. Blocks are colored white if they are the same size as the primary strain and get increasingly red or blue as the base pair size is smaller or larger, respectively, than that of the primary strain

 

Advanced Options

These options provide additional control over the analysis and its output.

Placement LOD threshold

Setting LOD threshold to a value greater than zero excludes markers from the analysis that have been placed on the map at a LOD score lower than the threshold value. This allows markers of lower confidence to be excluded from the analysis. NB - Not all maps have LOD score data available.

 

Basepair Range

This value controls how similar two allele sizes have to be in order to be considered the same size. The default is zero, ie. the two allele sizes have to be identical in order to be considered the same size. Setting the Basepair Range to a value greater than zero allows some flexibility in this calculation to allow for the potential that the reported allele sizes might not be accurate to the individual base pair. For example, setting the range to 2 means that if Allele size B is within +/- 2bp of Allele size A then it will be considered identical for the purposes of coloring the haplotype and calculating interstrain similarities.

 

Hide Size Data

Unchecking this option will show the individual allele sizes (in bp) for each marker in each strain on the visual haplotype report, this can be useful when one wants to know the precise values contained within the database as opposed to the size relative to another strain.

 

Document Contents

This allows control over the content of the returned PDF document:

Option Output
Tables & Haplotype PDF contains both the interstrain identity matrices and the visual haplotype
Only Visual Haplotype PDF contains only the visual haplotype
Only Strain Tables PDF contains only the interstrain identify matrices

 

Order Strains

This option controls the order of the strains (from left to right) on the interstrain relatedness matrix and the visual haplotype.

Option Effect
by % Identity Strains listed with Primary strain on the left, then others listed from left to right in order of decreasing percentage Identity
by % homology Strains listed with Primary strain on the left, then others listed from left to right in order of decreasing percentage homology
by Strain Name Strains listed in alphabetical order regardless of strain identity/homology. This option is useful when extracting data from multiple chromosomes as it keeps the strain order the same for each chromosome (assuming the same strains are selected).

 

Interstrain Distance Calculations

These options provide additional control over the sliding window used to calculate the interstrain relatedness.

Calculate distance with sliding window

Check box to chave the script calculate interstrain relatedness using a sliding window algorithm in addition to the basic identify calculation automatically performed. The sliding window algorithm attempts to add extra weight to conserved stretches of identical allele sizes as compared to the basic identity calculation which simply measures the overall percentage of alleles with identical sizes between two strains, regardless of location.

 

Window Size

The size of the window in cM or cR, as appropriate for the map selected.

 

Slide increment

The slide increment in cM or cR, as appropriate for the map selected. Determines how far up the chromosome the window is moved for each iteration of the analysis. Smaller values should give better resolution

 

Output Options

These allow selection of the overall data output format and the email account to which the output is sent.

Output Format

The PDF (Portable Document Format) is the defaul and recommend option. The file is generated offline following the submission of the request and the PDF file emailed to the supplied email address as an attachment. The XML option is somewhat experimental and currently only returns the allele size data for each marker in an XML format similar to that shown below:

<?xml version="1.0"    encoding="UTF-16" ?>
   <rgd_map_raw_data chromosome="19">
   <marker>
  	 <name>D19Rat2</name>
  	 <abs_distance>43.8598</abs_distance>
  	 <f_or_p>P</f_or_p>
  	 <lod>.2</lod>
  	 <allele_size strain="AVN/Orl">156</allele_size>
  	 <allele_size strain="BB/DP">166</allele_size>
  	 <allele_size strain="BB/DR">160</allele_size>
  	 <allele_size strain="BC/Cpbu">166</allele_size>
  	 <allele_size strain="BDIX/Han">154</allele_size>
  	 <allele_size strain="BDVII/Cub">166</allele_size>
  	 <allele_size strain="BN/Cub-lx">154</allele_size>
  	 <allele_size strain="BN/SsNHsd">154</allele_size>
  	 <allele_size strain="BP/Cub">166</allele_size>
  	 <allele_size strain="BUF/Pit">156</allele_size>
  	 <allele_size strain="COP/OlaHsd">156</allele_size>
  	 <allele_size strain="DA/Pit">156</allele_size>
  	 <allele_size strain="DONRYU/Melb">166</allele_size>
  	 <allele_size strain="F344/Pit">166</allele_size>
  	 <allele_size strain="FHH/Eur">156</allele_size>
  	 <allele_size strain="GH/Omr">166</allele_size>
  	 <allele_size strain="GK">154</allele_size>
  	 <allele_size strain="IS/Kyo">158</allele_size>
  	 <allele_size strain="LE/Mol">166</allele_size>
  	 <allele_size strain="LEW/Pit">156</allele_size>
  	 <allele_size strain="LH/Mav">166</allele_size>
  	 <allele_size strain="LOU/CHan">156</allele_size>
  	 <allele_size strain="M520/N">166</allele_size>
  	 <allele_size strain="MHS/Gib">166</allele_size>
  	 <allele_size strain="MNR/N">156</allele_size>
  	 <allele_size strain="MNRA/N">156</allele_size>
  	 <allele_size strain="MNS/Gib">166</allele_size>
  	 <allele_size strain="MR/Pit">156</allele_size>
  	 <allele_size strain="NEDH/K">166</allele_size>
  	 <allele_size strain="NP9">156</allele_size>
  	 <allele_size strain="ODU/N">158</allele_size>
  	 <allele_size strain="OKA/Wsl">166</allele_size>
  	 <allele_size strain="OM/Han">156</allele_size>
   	<allele_size strain="P5C">156</allele_size>
   	<allele_size strain="PVG/Pit">166</allele_size>
   	<allele_size strain="RGD_NAME">D19Rat2</allele_size>
   	<allele_size strain="SD/Rij">166</allele_size>
   	<allele_size strain="SHR/OlaHsd">158</allele_size>
   	<allele_size strain="SHRSP/Riv">164</allele_size>
   	<allele_size strain="SR/Jr">166</allele_size>
   	<allele_size strain="SS/Jr">166</allele_size>
   	<allele_size strain="SSLP_RGD_ID">35028</allele_size>
   	<allele_size strain="WAG/RijKyo">156</allele_size>
   	<allele_size strain="WF/Pit">166</allele_size>
   	<allele_size strain="WIST/Nhg">156</allele_size>
   	<allele_size strain="WKY/OlaHsd">164</allele_size>
   	<allele_size strain="WN/N">156</allele_size>
   	<allele_size strain="WTC/Kyo">164</allele_size>
   	<common_allele_data size="166" frequency="19" total_allele_num="48"
   	num_unique_alleles="8"/><allele_size strain="common">166</allele_size></marker>
   <marker>
   	<name>D19Rat102</name>
   	<abs_distance>48.1398</abs_distance>
   	<f_or_p>P</f_or_p>
   	<lod>.8</lod>
   	<no_acp_data/>
   </marker>
   <parameters>
		<map type="genetic" name="FHH x ACI, v7"/>
		<chromosome number="19"/>
		<flank1 distance="30"/>
		<primary_strain name="SHR/OlaHsd"/>
		<lod_threshold value="0"/>
		<bp_range value="0"/>
		<display table="table_haplotype" image_yn="no"
			font_size="twelve" homology_yn="1" order="by_percentage"
			color_scheme="normal"/>
		<homology window_size="10" slide_inc="5"/>
	</parameters>
</rgd_map_raw_data>

 

Your Email Address

The email address that the PDF document created by the application should be sent to.

 

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Related Information/Links

Detailed information on the microsatellite markers used by ACP Haplotyper can be found in the SSLP reports and are also refered to in the Strain reports for the various inbred strains. The Map reports provide a comprehensive list of all markers mapped on the various maps - SSLPs, ESTs, genes, etc.

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ACP Haplotyper Results

 

RGD: Genome Scanner Report Help

The ACP Haplotyper report is a multipage PDF document consisting of 4 major sections. To preserve the results in a readable format an annotated sample output is available which briefly describes the contents of the major sections and has detailed information on the visual haplotype section. The sample is taken from a report of chromosome 20 generated using SHRSP as the Primary Strain (colored blue), BN/SsnHsd as the secondary strain (colored red) based upon the radiation hybrid map v2.1.

View the annotated sample PDF output (Primary/Secondary Color scheme)

View the same haplotyper result colored using: Multicolored Scheme, Red/White/Blue color scheme.

 

 

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