27 May 2011

MULTIPLE SEQUENCE ALIGNMENT TOOL (CLASTAL W)


AIM
                                To find the evolutionary relationships between peptide sequences by performing Multiple sequence alignment using CLUSTAL W.

INTRODUCTION

                        Multiple sequence Alignments of protein sequences are important tools in studying tools. The basic information they provide is identification of conserved sequence. This is very useful in designing experiment to test and modify the function of specific proteins in predicting the function and structure of proteins and in identifying new protein families. Sequences can be aligned across (Global Alignment) or only in certain regions (Local Alignment).This is true for Pair wise and Multiple Alignments. Global alignments need to use gaps (representing insertions/deletions) while local Alignments can avoid them, aligning regions between gaps. CLUSTAL W is a fully Automatic program for global multiple sequence alignment of DNA and protein sequence. The alignment is progressive  and considers the sequences redundancy. Trees can also be calculated from Multiple Alignments. The program has some adjustable parameters with reasonable defaults.

CONSENSUS SYMBOL

                                          An Alignment while display by default the following symbols denoting the degree of conservation observed in each column.
(1)   *     It means that the residues or nucleotides in that column are identical in all sequences of the alignment.
(2)   :    It means that conserved substitutions have been observed , according to the color table above.
(3)    .     It means that semi-conserved substitutions are observed



INPUT SEQUENCES

Haliotis sorenseni
>gi|205943662|gb|ACI04728.1| lysin [Haliotis sorenseni]
EVALKVQIIAGFDRTLVKWLRTHGGTLSHVQKKALYFVNRRYMQTH

Haliotis walallensis

>gi|205943646|gb|ACI04720.1| lysin [Haliotis walallensis]
EVALKVQIIAGFDRTLVKWLRAHGRSLSHVQKKALYFVNRRYMQTH

Haliotis corrugata

>gi|205943630|gb|ACI04712.1| lysin [Haliotis corrugata]
EVALKVEIIAGFDRTLVKWLRVHGGRLSTVQKKALYFVNRRYMQTH

Haliotis rufescens

>gi|205943624|gb|ACI04709.1| lysin [Haliotis rufescens]
EVALKVQIIAGFDRGLVKWLRVHGRTLSTVQKKALYFVNRRYMQTH

Haliotis cracherodii           
                                                                                          
>gi|205943648|gb|ACI04721.1| lysin [Haliotis cracherodii]
EVALKVEIIAGFDRTLVKWLRNHGRGLNENQRKVLYFVNRRYMQTH

Haliotis iris

>gi|205943668|gb|ACI04731.1| lysin [Haliotis iris]
EVALKTQIIAGFDRKLASWLRRHGNRLSAIQKKTLYFVNRRYMQTH




PHYLOGENETIC TREES

(1)  Phylogram
                          Phylogram is a branching diagram trees assumed to be an estimate of phylogene, branch lengths are proportional to the amount of inferred evolutionary change.
(2)  Cladogram
                          Cladogram is a branching diagram (tree) assumed to be an estimate of a phylogene where the branches are of equal length. Thus Cladograms show common ancestry, but donot indicate the amount of evolutionary time separating taxa.

PROCEDURE
(1) Obtain the peptide sequence of given accession number from NCBI in FASTA format.
(2) Enter these sequences into the CLUSTAL W software in the given space.
(3) Adjust the required parameters.
(4) We run the CLUSTAL W tool.
(5) The Multiple sequence alignment thus obtained is interpreted.
(6) The phylogram and a cladogram obtained make interpretation of results easily.
  

Alignment Score --- 3486
 



  

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