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In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand Of DNA/RNA) Or amino acids (In protein sequences). A sequence logo Is created from a collection of aligned sequences And depicts the consensus sequence And diversity of the sequences. Sequence logos are frequently used to depict sequence characteristics such as protein-binding sites in DNA Or functional units in proteins.
DrawingDevice
01 Syntax
SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.SequenceLogo.DrawingDevice
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| DrawFrequency | 2 | Drawing the sequence logo just simply modelling this motif site from the clustal multiple sequence alignment. |
| E | 1 | The approximation for the small-sample correction, en, Is given by en = 1/ln2 x (s-1)/2n |
| InvokeDrawing | 1 | Drawing the sequence logo for the sequence motif model. |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| WordSize | 1 | The width of the character in the sequence logo.(字符的宽度) |
04 Members
DrawFrequency(
MotifPWM, String, Int32, String, Drivers)Drawing the sequence logo just simply modelling this motif site from the clustal multiple sequence alignment. (绘制各个残基的出现频率)
Parameters
| Name | Type | Description |
|---|---|---|
pwm | MotifPWM | The alignment export data from the clustal software. |
title | String | The sequence logo display title. |
DrawFrequency(
FastaFile, String, MotifPWM, Int32, Drivers)Drawing the sequence logo just simply modelling this motif site from the clustal multiple sequence alignment. (绘制各个残基的出现频率)
Parameters
| Name | Type | Description |
|---|---|---|
Fasta | FastaFile | The alignment export data from the clustal software. |
title | String | The sequence logo display title. |
E(
Int32, Int32)The approximation for the small-sample correction, en, Is given by en = 1/ln2 x (s-1)/2n
Parameters
| Name | Type | Description |
|---|---|---|
s | Int32 | s Is 4 For nucleotides, 20 For amino acids |
n | Int32 | n Is the number Of sequences In the alignment |
Drawing the sequence logo for the sequence motif model.
Remarks
(绘制SequenceLogo图)
Parameters
| Name | Type | Description |
|---|---|---|
model | DrawingModel | The model can be achieve from clustal alignment or meme software. |
frequencyOrder | Boolean | Reorder the alphabets in each residue site in the order of frequency values. default is yes! |
reverse | String | Reverse the residue sequence order in the drawing model? |
height | Boolean | height of the alphabet plot image |
WordSize
The width of the character in the sequence logo.(字符的宽度)