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IMC W702 Sequence Lane Tab Pane Description

The Sequence Lane tab pane allows you to set the scroll width of sequence lane, scale setting, font setting.

In addition, you can customize the notation of bases and amino acids displayed on Sequence Lane.

Sequence Scale Parameters section:

You can scroll the Sequence Lane, set tick marks, and set the grid.

Base Shift Left pull-down menu: Select the left scroll width of Sequence Lane from the pull-down menu. Select the left scroll width when the horizontal size of Sequence Lane is set to 1. With one mouse click, 1 scrolls the same width, ½ scrolls the width of 1/2 and 1/4 scrolls a quarter width.

Base Shigt Right pull-down menu: Select the left scroll width of Sequence Lane from the pull-down menu. Select the right scroll width when the horizontal size of Sequence Lane is set to 1. With one mouse click, 1 scrolls the same width, 1/2 is half width, 1/4 is right quarter width.

Interval of Scale Auto radio button: When you turn on the Auto radio button, the scale interval of the Sequence Lane is automatically set.

Interval of Scale Custom Radio Button: Turning on the Custom radio button allows you to set the scale interval of the Sequence Lane as desired.

Interval of Scale Custom Input field: Custom In the input field, enter the scale interval of Sequence Lane directly. You can enter any positive integer with bp.

Show Grid Line check box: When checked, the grid (dotted line) is displayed in the sequence lane.

Font section:

Font Size pull-down menu: You can select the font size of base letters and amino acid residue characters displayed in the sequence lane from the pull-down menu.

Amino acid character placement section: Base sequence on the sequence lane is displayed with one character each. Since the amino acid sequence corresponds to one codon (3 bases), one amino acid residue character is displayed in three bases. Specify on which letter the amino acid residue 1 character code is displayed among three codon characters.

Forward Strand pull-down menu: From this pull-down menu you can change the display position of amino acid residue on the forward chain of the sequence lane.

Reverse Strand pull-down menu: From this pull-down menu you can change the display position of amino acid residue on reverse complementary chain of sequence lane.

Codon Setting section:

Show Start Codon check box: When checked, the start codon candidate is displayed in the region for amino acid display of the sequence lane.

Show Start Codon color box: Sets the display color of the start codon candidate to be displayed in the sequence lane. The transparency of this color is automatically set, so the actual display color will be transparent.

Show Stop Codon check box: When checked, the stop codon is displayed in the region for amino acid display of the sequence lane.

Show Stop Codon color box: Sets the display color of the stop codon to be displayed in the sequence lane. The transparency of this color is automatically set, so the actual display color will be transparent.

Show Stop Codon Absent Region check box: When checked, displays a region where stop codon does not exist within the range of the specified number of bases or more.

Stop Codon Absent Length input field: Enter the minimum base length for making that region stop codon absent region. Enter a multiple of 3.

Show Stop Codon Absent Region color box: Specify the color for displaying stop codon absence area.

Show Amino Acid check box: When checked, the amino acid residue is displayed on the stop codon absence region.

Nucleotide Sequence Color section:

Change the color of base character.

A Color Box: Set the display character color of Adenine (Adenyne).

C color box: Set the display character color of cytosine (Cytosine).

G Color Box: Set the display character color of Guanine (Guanine).

T Color Box: Sets the display character color of thymine (Thymine).

M color box: Amino (Amino) Set the display character color of base.

R Color Box: Purine Set the display character color of base.

W Color Box: Weak Hydrogen Bonding (Weak) Set the display character color of base.

S Color Box: Strong Hydrogen Bonding (Strong) Set the display character color of base.

Y color box: Pyrimidine (Pyrimidine) Set the display character color of base.

K color box: Set the display character color of keto base.

V color box: Set the display character color of non-thymine (Not T) base.

H Color Box: Non-Guanine (Not G) Set the display character color of base.

D Color Box: Non cytosine (Not C) Set the display character color of base.

B Color Box: Set the display character color of non-adenine (Not A) base.

N Color Box: Unknown, Sets the display character color of any good bases.

X color box: Not used.

Amino Acid Color section:

Change amino acid residue character color.

A Color Box: Set the display character color of Alanine (Alanine).

R Color Box: Set the display character color of Arginine (Arginine).

N Color Box: Sets the display character color of asparagine (Asparagine).

D Color Box: Sets the display character color of aspartic acid (Aspartate).

C Color Box: Sets the display character color of Cysteine.

Q Color Box: Set the display character color of glutamine (Glutamine).

E Color Box: Set the display character color of glutamic acid (Glutamate).

G color box: Sets the display character color of glycine (Glycine).

H Color Box: Sets the display character color of Histidine (Histidine).

I color box: Sets the display character color of isoleucine (Isoleucine).

L Color Box: Sets the display character color of Leucine.

K Color Box: Set the display character color of Lysine (Lysine).

M color box: Set the display character color of methionine (Methionine).

F color box: Sets the display character color of phenylalanine (Phenylalanine).

P Color Box: Set the display character color of Proline (Proline).

S Color Box: Sets the display character color of Serine (Serine).

T Color Box: Set the display character color of Threonine.

W Color Box: Sets the display character color of tryptophan (Tryptophan).

Y color box: Set the display character color of tyrosine (Tyrosine).

V Color Box: Set the display character color of Valine (Valine).

U color box: Not used.

B Color Box: Sets the display character color of asparagine or aspartic acid (Asx).

Z color box: Sets the display character color of glutamine or glutamic acid (Glx).

X color box: Unknown, set any displayable character color of any good.

Show Complementary Color check box: When checked, when displaying base sequence characters, the character color is displayed in complementary colors of the specified color, and the background is displayed in character color.

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