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1. Software introduction

MUSCLE (Multiple Protein Sequence Alignment) is a software for protein-level multi-sequence alignment, which is superior to ClustalW in speed and accuracy. When doing multiple sequence alignments, MUSCLE is preferred in most cases. There are both local and online versions, and the online version is as follows: http://www.ebi.ac.uk/Tools/msa/muscle/.

2. The principle of algorithm.

Algorithm: MUSCLE first uses progressive alignment (progressive alignment) to obtain the initial multiple sequence alignment, and then uses horizontal alignment

Horizontal refinement iteration improves the results of multiple sequence alignment.

1) using k-mer counting method to construct global alignment and local similarity between sequences.

2) triangular matrix of distance between filling sequences

3) construct the sequence genetic tree by UPGMA or NJ method, and determine the root of the rootless tree.

4) the progressive alignment of the parent node is inferred upward from the leaf node, and finally the multiple sequence alignment of the root node is generated.

5) according to the multiple sequence alignment, the similarity between any two sequences is calculated.

6) calculate the Kimura distance matrix and construct the occurrence tree.

7) compare the difference between the newly generated tree and the original tree, if there is a rearrangement of nodes, jump to step 4

8) cut off a branch from the tree to produce two subtrees, each in descending order according to the distance from the root

9) calculate the multi-sequence alignment of two subtrees respectively, and compare the two results to get a new multi-sequence alignment.

10) if the SP score (sum of pairs) of the new comparison result decreases, keep the new comparison result, and vice versa

Discard it. Iterate 8-> 9-> 10 repeatedly until the score no longer decreases or the maximum number of iterations is reached.

3. Use the command

MUSCLE is very convenient to use. In most cases, users only need to specify input and output files.

$muscle-in file1-out file2

Example of input file:

> aATGAGGTAGAGATAGCCGG > bATGGTTAGCCGG

Example of the result file:

> aATGAGGTAGAGATAGCCGG > bATG----GTTAGCCGG

Run the program log:

MUSCLE v3.8.31 by Robert C. Edgar http://www.drive5.com/muscleThis software is donated to the public domain.Please cite: Edgar, R.C. Nucleic Acids Res 32 (5), 1792-97.12 seqs, max length 19 Avg length 1500 Iter 00 11 MB (- 1%) MB 1 100.00% K-mer dist pass 100 MB (- 1%) Iter 1 100.00% K-mer dist pass 20000 Iter 00 12 MB (- 1%) Align node00:00:00 12 MB (- 1%) Iter 1 100.00% Root alignment

4. Utilization of biological information

At present, muscle is mainly used in the evolutionary part of the genome, because to build the evolutionary tree and calculate the selection pressure, we need to align the sequence. Muscle is small and fast, so it is undoubtedly the best choice.

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