Strings 2008 2 4: Difference between revisions
ThomasHuber (talk | contribs) No edit summary |
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The similarity between two sequences are represented by comparison matrix. Each element in the matrix compares the character in one sequence with the character of the other sequence. Identical character pairings are visualised by a black pixel while different characters are coloured white. | The similarity between two sequences are represented by comparison matrix. Each element in the matrix compares the character in one sequence with the character of the other sequence. Identical character pairings are visualised by a black pixel while different characters are coloured white. | ||
The | The table below illustrates an example of a dot plot comparing DNA fragments of [http://en.wikipedia.org/wiki/Hemoglobin hemoglobin] from a person with [http://en.wikipedia.org/wiki/Sickle-cell_disease sickle-cell disease] and a healthy person. (This example can be generated interactively in class) | ||
{| class="wikitable" style="text-align:center" | |||
|+Multiplication table | |||
|- | |||
! × !! C !! T !! G !! A !! C !! T !! C !! C !! T !! G !! A !! G !! G !! A !! G !! A !! A !! G !! T !! C !! T !! G !! C !! C | |||
|- | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
! T | |||
| ||X || || || ||X || || ||X || ||X || || || || || || || ||X || ||X || || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! A | |||
| || || ||X || || || || || || || || || ||X || ||X ||X || || || || || || || | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
! T | |||
| ||X || || || ||X || || ||X || ||X || || || || || || || ||X || ||X || || || | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
! T | |||
| ||X || || || ||X || || ||X || ||X || || || || || || || ||X || ||X || || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! T | |||
| || || ||X || || || || || || || || || ||X || ||X ||X || || || || || || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! A | |||
| || || ||X || || || || || || || || || ||X || ||X ||X || || || || || || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! A | |||
| || || ||X || || || || || || || || || ||X || ||X ||X || || || || || || || | |||
! A | |||
| || || ||X || || || || || || || || || ||X || ||X ||X || || || || || || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! T | |||
| ||X || || || ||X || || ||X || ||X || || || || || || || ||X || ||X || || || | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
! T | |||
| ||X || || || ||X || || ||X || ||X || || || || || || || ||X || ||X || || || | |||
! G | |||
| || ||X || || || || || || ||X || ||X ||X || ||X || || ||X || || || ||X || || | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
! C | |||
| X || || || ||X || ||X ||X || || || || || || || || || || || ||X || || ||X ||X | |||
|} | |||
Revision as of 02:29, 17 January 2008
Visual comparison of strings
Humans are very good at identifying patterns visually. One of the first ways to compare biological sequences was to generate identity matrices and visualise them in a so called dot plot.
Computing of a dot plot
The similarity between two sequences are represented by comparison matrix. Each element in the matrix compares the character in one sequence with the character of the other sequence. Identical character pairings are visualised by a black pixel while different characters are coloured white.
The table below illustrates an example of a dot plot comparing DNA fragments of hemoglobin from a person with sickle-cell disease and a healthy person. (This example can be generated interactively in class)
× | C | T | G | A | C | T | C | C | T | G | A | G | G | A | G | A | A | G | T | C | T | G | C | C | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
C | X | X | X | X | X | X | X | T | X | X | X | X | X | X | G | X | X | X | X | X | X | X | A | X | X | X | X | C | X | X | X | X | X | X | X | T | X | X | X | X | X | X | C | X | X | X | X | X | X | X | C | X | X | X | X | X | X | X | T | X | X | X | X | X | X | G | X | X | X | X | X | X | X | T | X | X | X | X | G | X | X | X | X | X | X | X | G | X | X | X | X | X | X | X | A | X | X | X | X | G | X | X | X | X | X | X | X | A | X | X | X | X | A | X | X | X | X | G | X | X | X | X | X | X | X | T | X | X | X | X | X | X | C | X | X | X | X | X | X | X | T | X | X | X | X | X | X | G | X | X | X | X | X | X | X | C | X | X | X | X | X | X | X | C | X | X | X | X | X | X | X |
Discovery questions:
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Further (very advanced) reading for the Mathematics and Physics inclined
Recurrence plot of phase space trajectories
--ThomasHuber 14:02, 10 January 2008 (EST)