ClustalW2 Introduction

Once you have found all three correct sequences, you will want to try to align them to see how similar they are. We use the program ClustalW2 to do such an alignment. First, resplit your browser screen so you can tile the ClustalW2 site and this tutorial (to close your tiled pages select “Split” from the browser menu bar > select “Close all split browsers). Then re-split your screen between the tutorial and theĀ ClustalW2 site. Be sure to read the information below that describes ClustalW2. When you are finished, click the active link on the bottom of the page to bring up the site that hosts the ClustalW2 program.

ClustalW2

Multiple alignments of protein sequences are important tools in studying sequences. The basic information they provide is identification of conserved sequence regions. This is very useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins, and in identifying new members of protein families. Sequences can be aligned across their entire length (global alignment) or only in certain regions (local alignment). This is true for pairwise and multiple alignments. Global alignments need to use gaps (representing insertions/deletions) while local alignments can avoid them, aligning regions between gaps. ClustalW2 is a fully automatic program for global multiple alignment of DNA and protein sequences. The alignment is progressive and considers the sequence redundancy. Trees can also be calculated from multiple alignments. The program has some adjustable parameters with reasonable defaults.

ClustalW2 is a general purpose global multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

Multiple alignments of protein sequences are important tools in studying sequences. The basic information they provide is identification of conserved sequence regions. This is very useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins, and in identifying new members of protein families.

Sequences can be aligned across their entire length (global alignment) or only in certain regions (local alignment). This is true for pairwise and multiple alignments. Global alignments need to use gaps (representing insertions/deletions) while local alignments can avoid them, aligning regions between gaps. ClustalW2 is a fully automatic program for global multiple alignment of DNA and protein sequences. The alignment is progressive and considers the sequence redundancy. Trees can also be calculated from multiple alignments. The program has some adjustable features.

ClustalW2 Link:

http://www.ebi.ac.uk/clustalw/