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Clustal

This document provides an introduction to multiple sequence alignment using the Clustal software suite. It discusses the original Clustal program from 1988 and several subsequent versions, including ClustalV, ClustalW, ClustalX, and the latest ClustalOmega. These programs use progressive alignment methods and heuristic algorithms to efficiently align three or more nucleotide or protein sequences into a global multiple sequence alignment. The document also outlines the basic working principle of the Clustal alignment algorithm.

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Mohit Bagur
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110 views2 pages

Clustal

This document provides an introduction to multiple sequence alignment using the Clustal software suite. It discusses the original Clustal program from 1988 and several subsequent versions, including ClustalV, ClustalW, ClustalX, and the latest ClustalOmega. These programs use progressive alignment methods and heuristic algorithms to efficiently align three or more nucleotide or protein sequences into a global multiple sequence alignment. The document also outlines the basic working principle of the Clustal alignment algorithm.

Uploaded by

Mohit Bagur
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An Introduction to Multiple Sequence Alignment

1.1 Abstract: This paper aims to highlight the technology of multiple sequence alignment with Clustal
and provides a fairly fundamental guide to the technology at work.
Multiple sequence alignment refers to the process of aligning a sequence set, generally protein, DNA or
RNA. Because three or more sequences of biologically relevant length can be difficult and are almost
always time-consuming to align by hand, computational algorithms are used to produce and analyze the
alignments. These computational algorithms make use of heuristic methods and often incorporate
dynamic iterative workflows to yield accurate results. This paper discusses a few of the Clustal tools
presently in use to achieve alignment.

2.1 Clustal in use for MSA:

2.1.1 Clustal: The original program in the Clustal series of software was developed in 1988 as a way to
generate multiple sequence alignments on personal computers. This is written in Fortran and makes use
of a fast approximate algorithm to calculate similarity scores between sequences. The algorithm works
by calculating the similarity scores as the number of k-tuple matches between two sequences,
accounting for a set penalty for gaps. The more similar the sequences, the higher the score, the more
divergent, the lower the scores.

2.1.2 ClustalV: ClustalV was released 4 years later in 1992 and greatly improved upon the original,
adding and altering a few key features, including a switch to being written in C instead of Fortran like
its predecessor. Some of the most notable additions in ClustalV are profile alignments, and full
command line interface options. The ability to use profile alignments allows the user to align two or
more previous alignments or sequences to a new alignment and move misaligned sequences (low
scored) further down the alignment order. This gives the user the option to gradually and methodically
create multiple sequence alignments with more control than the basic option.

2.1.3 ClustalW: Released in 1994, ClustalW like the other Clustal tools is used for aligning multiple
nucleotide or protein sequences in an efficient manner. It uses progressive alignment methods, which
align the most similar sequences first and work their way down to the least similar sequences until a
global alignment is created. ClustalW is a matrix-based algorithm, and this program requires three or
more sequences in order to calculate a global alignment.

2.1.4 ClustalX: ClustalX features a graphical user interface and some powerful graphical utilities for
aiding the interpretation of alignments and is the preferred version for interactive usage since 1997.
Users may run Clustal remotely from several sites using the Web or the programs may be downloaded
and run locally on PCs, Macintosh, or Unix computers.

2.1.5 ClustalOmega: Clustal Omega is the latest addition to the Clustal family. It offers a significant
increase in scalability over previous versions, allowing hundreds of thousands of sequences to be
aligned in only a few hours. Clustal Omega is able to read sequence input in various formats. These are
a2m/Fasta, Clustal, msf, phylip, selex, Stockholm, and Vienna.
3.1 Working principle:

Steps for CLUSTAL algorithm

 Calculate all possible pairwise alignments, record the score for each pair.
 Calculate a guide tree based on the pairwise distances (algorithm: Neighbor Joining).
 Find the two most closely related sequences
 Align the sequences by progressive method
i. Calculate a consensus of this alignment
ii. Replace the two sequences with the consensus
iii. Find the two next-most closely related sequences (one of these could be a
previously determined consensus sequence).
iv. Iterate until all sequences have been aligned
 Expand the consensus sequences with the (gapped) original sequences
 Report the multiple sequence alignment

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