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How to work with genetic traits files

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Table of Contents

What is Traits files?
Wherefore I need Traits files?
Where I can find the samples of Traits files?
Can I edit samples files or create new Traits files and use them in the program?
What program is needed for editing or creating Traits files?
How to open Traits file in the program?
How works the Traits file?
How to write parental genotypes using Traits file?
How to get the results of cross for traits from Traits file?
How to see from what kind of genotypes consists the specific phenotype in a ratio of Traits phenotypes?
What are the basic rules for writing Traits file?
What is the writing order of alleles in Traits file?
How to write correctly a simple Traits file using the basic rules?
Can I write alleles in the Traits file , which are marked with multiple letters?
Why is it so important is the writing order of alleles in Traits file?
How to write Traits file correctly, if you are using a "+" or "<+>" for marking the phenotype of wild-type?
From what formed the ratio of Traits phenotypes?
When you can't check-on the checkbox "From phenotypes"?
How to write Traits file correctly for incomplete dominance and codominance?
How to write Traits file correctly for dominant epistasis?
How to write Traits file correctly for recessive epistasis?
How to write Traits file correctly for polygenic inheritance?
Is it possible to mark a trait in Traits files as number?
What does mean the symbol "*" in Traits files?
What does mean the symbol "!" in Traits files?

Answers

Q: What is Traits files?
A: It is simple text files with the "txt" extension and encoded in Utf-8. The data in these files has a certain structure. [Back to the top]

Q: Wherefore I need Traits files?
A: Traits files needed to solve genetic problems with allelic (incomplete dominance and codominance) and nonallelic interactions (epistasis). However, they can be used to solve simple genetic problems. [Back to the top]

Q: Where I can find the samples of Traits files?
A: If you do not change the destination folder during installation, these files are located in "C:\Program Files\Bifido Punnett Square Calculator\Traits files"(directory for traits files). [Back to the top]

Q: Can I edit samples files or create new Traits files and use them in the program?
A: Yes. But remember, that files must be encoded in Utf-8. [Back to the top]

Q: What program is needed for editing or creating Traits files?
A: You can use a simple text editor such as Notepad. Do not use for creating these files, word processors, such as Microsoft Word. [Back to the top]

Q: How to open Traits file in the program?
A: Choose the tab "Traits". Click "Open" button and you'll see the standard Windows dialog to select the file. By default the program will open the folder with the samples of Traits files. If your file is located elsewhere, you can use this window to find your file and open it. If the file is made incorrectly you may get an error message. [Back to the top]

Q: How works the Traits file?
A: Traits file consists of two parts. After opening Traits file you will see the data in two tables, "Traits" and "Genes combinations". Table "Traits" is filled with data from the first part of the file. In the first column (Gene) of table "Traits" will be alleles, while in the second column (Trait) - the traits, which correspond to them. Table "Genes combinations" is filled with data from the second part of the file. Entries in the second part of the Traits file enclosed in the symbols "{" and "}". In the first column "Names" of table "Genes combinations" will be the names of traits, and in the second column - "Combinations" will be presented the combinations of alleles, that control this trait. The second part of Traits file is intended for the formation of parental genotypes for crossing. This part is not optional, but it makes work more comfortable. [Back to the top]

Q: How to write parental genotypes using Traits file?
A: Using the table "Genes combinations" you can choose parental genotypes for crossing. If you do the mouse click on a cell in the column "Combinations", you will see a list of all possible combinations of alleles for this trait. So you can choose the necessary value for each trait. By clicking "To First" or "To Second" you can copy the selected combination into the text box for the first or second parental genotype. This method of forming the parental genotypes is made in the program in order to avoid errors and for more comfortable work. You may not use this method, but simply write the parents genotypes in the corresponding text boxes. [Back to the top]

Q: How to get the results of cross for traits from Traits file?
A: Once you have opened Traits file and wrote the parents genotypes in the text boxes, you must choose the "Traits phenotypes" for the crossing results, and push "Calculate results" button. On the tab "Calculator" you will see the result - the ratio of Traits phenotypes. [Back to the top]

Q: How to see from what kind of genotypes consists the specific phenotype in a ratio of Traits phenotypes?
A: Choose the "Find" tab. Using the table "Find" you can choose parental specific phenotype. If you do the mouse click on a cell in the column "Combinations", you will see a list of all possible combinations. So you can choose the necessary value for each trait. After pushing "Find" button in the right table you will see from what kind of genotypes consists this particular phenotype. [Back to the top]

Q: What are the basic rules for writing Traits file?
A:
1) For division groups of traits use empty string.
2) For division alleles and trait use colon simbol ":".
3) For division alleles use space simbol " ".
4) For definition the second part of Traits file use simbols "{" and "}".
[Back to the top]

Q: What is the writing order of alleles in Traits file?
A:
1) Write dominant allel first and recessive allel after.
2) Write alleles for traits with genes interactions before trait with simple dominant allel.
3) Write nonallelic genes interactions (Epistasis) before allelic genes interactions (Incomplete and codominance).
[Back to the top]

Q: How to write correctly a simple Traits file using the basic rules?
A: Let's consider it on concrete example. Using Windows explorer or any other file manager go to the folder "C:\Program Files\Bifido Punnett Square Calculator\Traits files"(directory for traits files). And then open the file "Mendelian 1.text" in a plain text editor like Notepad: We first consider the first part. We have three groups of traits - color, size and length. These groups are separated by blank lines (empty strings):

Y:Yellow
y:green

B:Big
b:smoll

L:Long
l:short

Each line in this group it's allele and trait, which are separated by a colon:

Y:Yellow

In each group, the dominant allele is written first, and below the recessive:

Y:Yellow
y:green

The second part of Traits file enclosed in the symbols "{" and "}" and separated from the first by empty string:

{
color:Y y
size:B b
length:L l
}

Each line here it's the name of trait and all alleles of a gene, that controls this trait. They are separated by a colon too:

color:Y y

And alleles of the gene are separated by a space character:

Y y

[Back to the top]

Q: Can I write alleles in the Traits file , which are marked with multiple letters?
A: Yes. You can see this in file "Mendelian 2.txt". [Back to the top]

Q: Why is it so important is the writing order of alleles in Traits file?
A: The program processes Traits file from top to bottom. From each group of traits, the program selects only one trair for each genotype and then moves to the next group. So, what trait the program will choose - depends on the order of alleles in the Traits file. If the allele or combination of alleles is dominate over other alleles, it must placed above in order in the Traits file. The only exception - "+" or "<+>" - this trait can be written at the end of each group. [Back to the top]

Q: How to write Traits file correctly, if you are using a "+" or "<+>" for marking the phenotype of wild-type ?
A: In this case, you must observe a few simple rules:
1) Each group of traits must include the trait, that correspond to - "<+>". This trait can be written at the end of each group.
2) Signs which are recessive in relation to the "<+>" should be written as a pair of alleles.
You can see this in file "Mendelian 3.txt"
[Back to the top]

Q: From what formed the ratio of Traits phenotypes?
A: The program generates the ratio of Traits phenotypes by the ratio of genotypes or phenotypes. If the checkbox "From phenotypes" is not checked, then the ratio is formed by the ratio of genotypes and, if checked, then by the ratio of phenotypes. [Back to the top]

Q: When you can't check-on the checkbox "From phenotypes"?
A: If you're dealing with incomplete or codominance, or if you use "+" sign to mark the alleles. [Back to the top]

Q: How to write Traits file correctly for incomplete dominance and codominance?
A: The combination of alleles for partial dominance and codominance dominate over simple dominant allele and over recessive allele. Therefore, this combination should be written before the dominant and recessive alleles. For example, like this:

A a:trait1
A:trait2
a:trait3

{
name:A a
}

[Back to the top]

Q: How to write Traits file correctly for dominant epistasis?
A: The dominant epistatic allele or complementary alleles dominate over simple dominant or recessive alleles, and over the combination of alleles for incomplete dominance and codominance. Therefore, the dominant epistatic allele, or a combination of complementary alleles need to write before any hypostatic alleles. For example like this:

A B:trait1
A:trait2
B:trait3
*:trait4

{
name:A a
name:B b
}

[Back to the top]

Q: How to write Traits file correctly for recessive epistasis?
A: If the program generates the ratio of Traits phenotypes by the ratio of genotypes, the recessive epistatic allele need to write as a pair. Recessive epistatic alleles dominate over simple dominant or recessive alleles, and over the combination of alleles for incomplete dominance and codominance. Therefore, the recessiveepistatic allele need to write before any hypostatic alleles. For example like this:

b b:trait1
A:trait2
a:trait3

{
name:A a
name:B b
}

[Back to the top]

Q: How to write Traits file correctly for polygenic inheritance?
A: For the polygenic inheritance the traits will be placed in order of decreasing number of polygenes. For example like this:

A A A A:trait1
A A A:trait2
A A:trait3
A:trait4
a:trait5

{
name:A a
name:A a
}

[Back to the top]

Q: Is it possible to mark a trait in Traits files as number?
A: Yes.It is used to mark traits in some genetic problems with the polygenes. For example:

D:Value for dominant allel
d:Value for recessive allel

{
name:D d
name:D d
}

[Back to the top]

Q: What does mean the symbol "*" in Traits files?
A: This symbol is denotes any other allele except for alleles that are written before that character in the Traits files. But if this trait is marked as number, then the symbol "*" in this case denotes a certain base value for the homozygous recessive genotype. It is used in polygenic inheritance, when added to the base value - values of the alleles, that are placed before this character in the Traits files. This symbol can be used in Traits files starting with version 3.3. For epistasis it might look like this:

A B:trait for this allels combination
*:trait for all other alleles

{
name:C c
name:P p
}

And for polygenic inheritance like this:

D:Additional value for each dominant allel
*:Base value for recessive genotype

{
name:D d
name:D d
}

[Back to the top]

Q: What does mean the symbol "!" in Traits files?
A: This symbol is used in genetic problems for polygenic inheritance or linked inheritance in the second part of Traits files. For polygenic inheritance, we use this symbol to insert a colon in the "Genes combinations" before and after our genes ( Starting with version 3.3 this should be done only if you mark alleles with different letters, such as "R" - the dominant allele and "t" - a recessive allele). If you put that character before the name of trait, then, in the "Genes combinations", instead of all possible combinations of alleles for this trait - will be just these alleles or values. This can be useful for Traits files with linked inheritance in order to correctly form the parental genotypes. For example:

A:trait1
a:trait2

B:trait1
b:trait2

{
!simbol:(
!name1:A a
!name2:B b
!simbol:)
!simbol:(
!name1:A a
!name2:B b
!simbol:)
}

[Back to the top]

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