Lettuce genetic map viewer

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High-Throughput Mapping Pipeline Of EST Based
Sequences On Lettuce Genome. Genetic Map
Validation, Visualization And Web
Presentation. Alexander Kozik , Steve Edberg ,
Barnaly Pande , David Caldwell , David Lee ,
Travis Kleeburg , Fallon Chen , Richard
Michelmore Genome Center,
University of California Davis CA 95616
Identification of putative polymorphism and oligo
design
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Marker (Contig/EST) selection (gene of interest)
http//cgpdb.ucdavis.edu/
Efficient genetic mapping of large numbers of
markers requires the coordination of the efforts
of several people each of whom are responsible
for different parts of the operation. We have
developed a pipeline to map new markers on high
density genetic maps. Major goals and features of
this pipeline are A) Minimizing the number of
steps from experimental data generation to entry
of data into database. B) Automatic error
checking and error handling of spreadsheets that
contain marker descriptions and raw scores, prior
to uploading into the database. C) Simplified and
controlled data flow to and from database for
mapping procedures. This pipeline includes i)
Python Contig Viewer for semiautomatic search of
EST candidates with putative polymorphisms and
automatic design oligonucleotide primers for
selected sequences relative to potential intron
positions. ii) Scripts that provide controlled
dataflow from spreadsheets into our relational
mySQL database. iii) Web interface (Dendrogram
Viewer) to manipulate data in database and
pre-select sets of markers for further mapping
while maintaining linkage group designations from
earlier maps. iv) Visualization tools
(CheckMatrix) to perform quality control and
validate maps. v) Web interface to display
results of mapping graphically. Our database
(http//cgpdb.ucdavis.edu/) provides
functionality to compare several genetic maps
simultaneously as well as the raw data that were
used to construct the genetic maps. These scripts
are publicly available.
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Python ContigViewer
http//cgpdb.ucdavis.edu/SNP_Discovery/Py_ContigVi
ewer/
Entering raw scores data and marker information
into database
MS Excel templates with defined fields. Error
checking using custom Python scripts.
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MAPPING USING JOINMAP AND CUSTOM PROGRAMS
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http//cgpdb.ucdavis.edu/database/genome_viewer/vi
ewer/

• Pairwise comparison
• (finding recombination/LOD score values for
  all pairs of markers)
• (Tools custom Python scripts or JoinMap)

Web interface to access Lettuce genetic maps
http//cgpdb.ucdavis.edu/XLinkage/Genetic_Map_PyMa
d_Matrix.html
2. Group analysis (assigning particular
markers to specific chromosomes) (Tools PHP
Dendrogram Viewer)
Map and linkage group selection
gt Decreasing recombination value threshold gt
3. Pairwise comparison within each group
(Tools JoinMap)
4. Mapping (Tools JoinMap)
5. Validation of constructed map using
CheckMatrix (custom Python scripts)
Query submission and data visualization
http//cgpdb.ucdavis.edu/XLinkage/
6. Map data entering into database
Dendrogram Viewer manipulates data in the
database and selects set of markers for further
mapping while maintaining linkage group
designations from earlier maps. Basically it
performs group or clustering analysis.
Zoom-in functionality into selected region
Detailed information about selected marker
Lettuce genetic map viewer is written in PHP and
uses GD library. The viewer interacts with tables
in the relational mySQL database and creates
graphical output dynamically.
CheckMatrix 2D plot validation of map
quality (web link to large image)
Displaying and comparing of several different
maps simultaneously
CheckMatrix 2D plot is a set of Python scripts to
visualize and validate genetic maps. Required
input files 1. Genetic map 2. Recombination
scores 3. Raw marker scores Output 1.
CheckMatrix diagonal 2D plot of all markers
versus all markers. Color gradient reflects
linkage / recombination scores Red strong
linkage Yellow weak linkage Black no
detectable linkage. 2. Visualization of raw
scores where all markers ordered as on genetic
map. Markers with high number of double
crossovers are candidates for re-checking of raw
scores or map position.
Purpleframework markers
CheckMatrix source code and detailed description
is available at
Allele composition
http//cgpdb.ucdavis.edu/XLinkage/