User Manual
GenoPlayer input data
GenoPlayer requires two simple input files in text (ASCII) format.- A locus file containing marker names and raw marker scores.
- A linkage file with marker names and marker positions on a linkage map.
Several linkage groups can be included in a single file.
Locus file:
(1) Locus file is a plain text file containing marker names followed by tab delimited white space, and then raw marker scores. The data format is similar to Joinmap output.
(2) The first line in the 'locus file' must contain name of the experiment entered in the format, "name = trial"
(3) Notes and comments related to the experiment can be entered on subsequent rows, but must begin with semicolon (;).
Example of Locus file:
name = trial
;comment1
;data type f2 intercross
;8 50 13
marker14
DHBHHADAADBADBHHDBHHBBDHHADDBAHDAHHBHAABABDAHHBBHH
marker30
AHBAHBBBHABBAHAABHBBHHHBBHHHHBAHABHHHHAHHHAHBBAHA-H
marker35
BHHDHAABHDHHBHHABABBAAAABHBHHDHHBBDCHDHDHHBAHBA-DA
marker37
AHBHDAAAHBBHAAHDAHHBBBBAHHDBAAAHAADBHBABABHHDDHHAA
marker43
CHHHHBDAACCHHCACHHAABBHAABAHHBHCBAACABBBHCABCBHCDB
marker52
AHABBHHCAHHAAABCHAHHABHBHHBAHHACHBHBACHCHHAHBAACHA
marker65
BBHCAHAABHAHHBHHABABBAAAHBCCBCHHHABACAHHAABBHHA-HA
marker80
BHAAHBBHAHBDABHHBABDABBBHCBHAH-BHHAHABHA-HAHBBADHA
Linkage or map file
The linkage file is a plain text file (ASCII) containing two columns of data. First column contains linkage group number and marker names in that group. Second column contains map positions. Marker names and corresponding map position are separated by tab delimited white space.
Example of linkage or map file
chromosome 1
marker52 0
marker43 21.5
marker112 31.6
marker35 53.7
marker65 69.2
marker270 80.8
chromosome 2
marker519 0
marker466 43.1
marker14 57.1
marker437 67.1
marker137 81.2
marker535 110.9
marker124 126.5
marker85 135.7
chromosome 3
marker86 0
marker397 8.5
marker80 28.1
marker141 45.7
marker350 77.7
marker212 45.2
GenoPlayer web access:
The GenoPlayer program is accessible over the web. The data (input) files can be uploaded by clicking on the browse button. Linkage file should be uploaded first followed by the locus file.
GenoPlayer output:
GenoPlayer program can display data by (1) linkage group (2) individual genotype (3) subset of individuals (4) all individuals and (5) all linkage groups.
Linkage group:
The default mode is set to selection by 'linkage group' option. This option will show all individuals next to each other in the linkage group selected. Linkage groups can be selected by using the drop down list. (Fig 1)
Individual genotype:
Individual genotype option is available to view all linkage groups per individual. Desired individuals can be selected using the drop down list (Fig 2).
Subset by linkage group:
A subset of individuals in a particular linkage group can be selected by using the drop down selection list. Random individual numbers (not continuous) can be selected by holding down the 'Ctrl' button and clicking the right mouse button The drawing shows recombination cross-over points as black circles. Caution should be taken when interpreting crossover events as the exact crossover position is not known and GenoPlayer only highlights the most probable crossover positions. Summary line indicates the total number of cross-overs within each interval (Fig 3). Summary of total number of cross-overs, maximum interval, minimum interval and average interval can be obtained by checking the "summary option" button and clicking on "draw" button (Fig 4).
All linkage groups:
Graphical genotypes of all individuals and all linkage groups can be viewed in this option (Fig 5).
Subset of all linkage groups:
By selecting this option, user can view graphical genotypes of a subset of population or individuals selected. Black circles indicate recombination cross-over positions and summary line indicates the total number of cross-overs at each interval (Fig 6). When the summary option is selected and clicked on the draw button, GenoPlayer generates summary lines with cross-over points and a summary table of total number of cross-overs, maximum interval, minimum interval and average interval for each linkage group (Fig 7).
Details of individual locus:
Information about any locus including the neighboring loci and map position can be obtained by Double clicking on any locus on GenoPlayer output drawings (Fig 8).
Query option:
GenoPlayer program can display individuals selected on their genotypic composition expresses as proportions of parental alleles. User can select individuals with genotypes A, A or D, A or D or H, B or C or H, B or C, and B with allele composition of more than 60%, 70%, 80%, 90% and 95%. Fig. 9 shows GenoPlayer output drawing of individuals containing more than 60% of genotype A.
Color coding options:
GenoPlayer program uses red for genotype A, orange for genotype D (not A), yellow for H or heterozygous, light green for genotype C (not A), blue for genotype B and white for unknown. User can use the default options or can define the color coding for each genotype by clicking on the color square and select the desired color for that genotype from the full color range.
Statistics:
Statistics about the estimated genome composition are calculated for all the five options in GenoPlayer. Summation of allele frequencies are shown on the window below the graphical genotypes. Summary table of total number of cross-overs, maximum interval, minimum interval and average interval for each linkage group can be obtained by selecting the options 'subset by linkage group' and 'subset of all linkage groups'.
Image saving and printing:
GenoPlayer output images can be saved and printed by selecting buttons on the output window. Alternatively, the drawings can be captured using 'print screen' on the key board and pasted in other image editing programs.
Contact information:
Please write your questions and comments to Padma Sudarshana at sudarshana@vegmail.ucdavis.edu.
References:
T. J. Vision, D. G. Brown, D. B. Shmoys, R. T. Durrett and S. D. Tanksley. 2000. Selective Mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 155:407-420.
Copyright © 2003 University of California at Davis
|