Multiple sequence alignment: Difference between revisions

Revision as of 17:41, 18 April 2020

Revision as of 10:45, 20 April 2020

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===Mathematical definition===

Given <math>m</math> sequences <math>S_i</math>, <math>i = 1,\cdots,m</math> similar to the form below:

<blockquote>

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</blockquote>

A MSAmultiple sequence alignment is taken of this set of sequences <math>S</math> by inserting any amount of gaps needed into each of the <math>S_i</math> sequences of <math>S</math> until the modified sequences, <math>S^'_i</math>, all conform to length <math>L \ge \max\{x_in_i \mid i = 1,\ldots,rm\}</math> and no values in the sequences of <math>S</math> of the same column m, consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below:

<blockquote>

<math>

S^' :=

\begin{cases}

S^'_1 = (S^'_{11},S^'_{12},\ldots, S^'_{1L}) \\

S^'_2 = (S^'_{21},S^'_{22},\ldots, S^'_{2L}) \\

\,\,\,\,\,\,\,\,\,\,\vdots \\

S^'_m = (S^'_{r1m1},S^'_{r2m2},\ldots, S^'_{rLmL})

\end{cases}

</math>

</blockquote>

To return from each particular sequence <math>S^'_i</math> to <math>S_i</math>, remove all gaps.

==Graphing approach==