Identifying Sequence Conservation

The ClustalW database is part of the EMBL European Bioinformatics Institute Webpage. This program allows you to align different sequences in order to identify regions of homology between proteins. Any proteins can be compared to one another. For example, proteins with similar functions in different species or proteins from the same family in a single species can be compared in order to find homologous sequences.

At first glance it seems that BlastN and ClustalW both perform the similar function of finding homology among different sequences, however, it is important to realize that each database functions in a very different way. BlastN performs what is known as a "one-against-all" search where your sequence of interest is compared to every sequence contained in the database. ClustalW is slightly different in that it performs a "many-against-each-other" search and directly compares only the sequences you interested in studying against themselves. For that reason, ClustalW is a much more specific database tool to use when studying sequence homology in greater detail.

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