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How to use Clustal for multiple sequence alignment, I believe many inexperienced people are helpless about this, this article summarizes the causes and solutions of the problem, through this article I hope you can solve this problem.

Multiple sequence alignment plays an important role in many fields such as conservative region identification, phylogenetic analysis, motif recognition, etc. It is one of the essential skills for bioinformatics data analysis. Clustal is a classic multi-sequence alignment tool that supports DNA, RNA, protein alignment.

There are two versions of cluster available, the previous version provides both GUI and command line tools, the GUI version is called ClustalX, the command line version is called ClustalW; the latest version is called Omega, only the command line version is available.

The latest version of omega alignment is more accurate and faster, suitable for multiple sequence alignments of thousands of pieces, and the software is currently only available in command-line versions. On the official website, source code and compiled binary files are provided.

Usually, download the binary executable file directly. The basic usage of the software is as follows:

clustalo -i seq.fasta > align.fa

-i Specifies the input sequence file, default output is printed on screen, can be redirected to the specified file. The software supports multiple formats of output

fasta

clustal

msf

phylip

selex

stockholm

vienna

The default output format is fasta, and you can specify the output file format with the--outfmt parameter. Multiple sequence alignment differs from Blast in that Blast is a local alignment, while multiple sequence alignment is a global alignment. Global alignment means that input sequences need to be aligned to the same level, usually by inserting bases into the input sequences to align the sequences, as shown below

>ENA|CAA23748|CAA23748.1 Homo sapiens (human) alpha globinATGGTGCTGTCTCCTG----CCGACAAGACCAACGTCAAGGCCGCCTGGGGTAAGGTCGGCGCGCACGCTGGCGAGTATGGTGCGGAGGCCCTGGAGAGGATGTTCCTGTCCTTCCCCACCACCAAGACCTACTTCCCGCACTTC---GACCTGAGCCACGGCTCTGCCCAAGTTAAGGGCCACGGCAAGAAGGTGGCCGACGCGCTGACCAACGCCGTGGCGCACGTGGACGACATGCCCAACGCGCTGTCCGCCCTGAGCGACCTGCACGCGCACAAGCTTCGGGTGGACCCGGTCAACTTCAAGCTCCTAAGCCACTGCCTGCTGGTGACCCTGGCCGCCCACCTCCCCGCCGAGTTCACCCCTGCGGTGCACGCTTCCCTGGACAAGTT---CCTGGCTTCTGTGAGCACCGTGCTGACCTCCAAATACCGTTAA>ENA|CAA24095|CAA24095.1 Mus musculus (house mouse) alpha-globinATGGTGCTCTCTGGGGAAGACAAAAG----CAACATCAAGGCTGCCTGGGGGAAGATTGGTGGCCATGGTGCTGAATATGGAGCTGAAGCCCTGGAAAGGATGTTTGCTAGCTTCCCCACCACCAAGACCTACTTTCCTCACTTTGATGT---AAGCCACGGCTCTGCCCAGGTCAAGGGTCACGGCAAGAAGGTCGCCGATGCGCTGGCCAGTGCTGCAGGCCACCTCGATGACCTGCCCGGTGCCTTGTCTGCTCTGAGCGACCTGCATGCCCACAAGCTGCGTGTGGATCCCGTCAACTTCAAGCTCCTGAGCCACTGCCTGCTGGTGACCTTGGCTAGCCACCACCCTGCCGATTTCACCCCCGCGGTACATGCCTCTCTGGACAAATT---CCTTGCCTCTGTGAGCACCGTGCTGACCTCCAAGTACCGTTAA>ENA|BAA20512|BAA20512.1 Cyprinus carpio (common carp) alpha-globinATGAGTCTCTCTGATAAGGACAAGGCTG----CTGTGAAAGCCCTATGGGCTAAGATCAGCCCCAAAGCCGATGATATCGGCGCTGAAGCTCTCGGCAGAATGCTGACCGTCTACCCTCAGACCAAGACCTACTTCGCTCACTGGGATGACCTGAGCCCTGGGTCCGGTCCTGTGAAGAAGCATGGCAAGGTTATCATGGGTGCAGTGGCCGATGCCGTTTCAAAAATAGACGACCTTGTGGGAGGTCTGGCCTCCCTGAGCGAACTTCATGCTTCCAAGCTGCGTGTTGACCCGGCCAACTTCAAGATCCTCGCACACAATGTCATCGTGGTCATCGGCATGCTCTTCCCTGGAGACTTCCCCCCAGAGGTTCACATGTCAGTTGACAAGTTTTTCCAGAAC---TTGGCTCTGGCTCTCTCTGAGAAGTACCGCTAA

Alignment of sequences by inserting-into sequences. If you're not used to the command-line approach, there are online services available. EBI offers online services at the following addresses:

https://www.ebi.ac.uk/Tools/msa/clustalo/

It is very simple to use, enter the sequence, adjust the parameter settings, and then submit it. In the output results, color labeling and evolutionary tree visualization are also provided.

Visualize the results of multiple sequence alignment through Mview, as shown below

Export to Jalview software for visualization is also supported.

Phylogenetic Tree allows you to view the results of the Phylogenetic Tree. By default, the NJ method is used to build trees. The diagram is as follows

You can also create a phylogenetic tree by sending to Simple Phylogeny, which supports both NJ and UPGMA methods.

After reading the above, do you know how to use Clustal for multiple sequence alignment? If you still want to learn more skills or want to know more related content, welcome to pay attention to the industry information channel, thank you for reading!

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