QGene is a Macintosh software application written for the visualization and rapid statistical analysis of molecular-marker and phenotypic trait data. Following is a short description of what a first-time user will want to know about supplying data to QGene.
QGene can read datafiles with the variables (traits or markers) in either rows or columns. A second file is prepared for map data and symbol specifications that QGene needs.
&Line/ L1 L2 L3 L4 L5 L6 L7 L8 L9
L10 L11 L12 L13 L14 L15 L16 L17 L18 L19 L20 L2L1 L22 L23 L24
&Family\ 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 5 5 5 5 6 6 6 6
*PBS128 110011110130101000001133
*CDO1379 100101111010011110000033
*BCD718a 110110000110110111100133
*BCD718e 111011111111011111110033
*ABG460a 111110011101101111111133
^Yield 1.5 - .95 .64 .78 - 2.03 1.24 - - 1.29 - - - .89 .38 .97
1.96 1.46 .05 - .75 .82 1.11
^Trait2 1.25 .59 1.27 1.13 .76 .31 2.78 1.43 .16 .52 1.07 .29
.74 .27 1.76 .82 .74 2.18 1.54 .0 .46 1.09 .72 .54
^Trait3- 1.42 0.51 1.24 1.36 .78 .44 2.64 1.7 .24 .56 .87 .54
.9 .25 1.55 1.06 .84 1.64 .95 1.18 .46 .75 .9 1.9
&PA PA PA PA PA PA PA NY NY NY NY NY NY NY MI MI MI MI MI
MI MI MI #NY #MI
The & leader refers to a categorical trait and the ^ to a metric one; the * indicates a marker, the / and \ trailers following the name of a "&" trait tell QGene to use the entries as individual and family names, and the # in the last (or any other) categorical trait shows that the labeled genotypes are to be considered controls and omitted from marker analyses.
Standard population types are dhf1, ri, bc1f1, bc2f1, bc3f1, bc1f2, bc2f2, f2, f3, bc1s1, bc1s2, or bc2s1. Marker genotype codes used in the datafile represent homozygote AA, homozygote aa, heterozygote Aa, ambiguous dominant markers a_ and A_, and missing data. For those familiar with Mapmaker, this is the same scheme. An additional 9 character codes (not shown here) have been added in version 3.0 for crosses with up to four alleles segregating, designated by type HxHf1.The map file for the above data file is as follows:
data type dhf1
24 5 6 2 10xxx3
parents M-1 Ciano
*3A 2 PBS128 21.3 CDO1379
*3B 3 ABG460a 34.2 BCD718a 18.1 BCD718e
This tells QGene that the doubled-haploid population derived from the cross of M-1 with Ciano has 24 individuals and has been characterized for 5 markers and 6 traits, with the markers being placed on two chromosomes and the only three valid genotype codes (two homozygotes and the missing-data symbol) being 1, 0, and 3. The last two lines give QGene map information. The number following a chromosome name gives the count of the markers on that chromosome, while numbers between marker names signify interval sizes in centimorgans.
A dataset may have as many as 2048 markers, 2048 individuals, and 500 traits, and you may load as many datasets as memory will allow. For a sizable dataset of 115 individuals, 800 markers, and 200 traits, 2.5 Mb of application memory was adequate. Of course memory can be readily increased from the Finder.
When you load a dataset you'll see a window like the one at right containing a list of the traits in the set.
You may publish any text or graphical output from QGene in original or adapted form. It is expected only that such material be presented and attributed in such a way that it's reasonably apparent that QGene was the original source. The proper citation is given in the program's About... box.
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