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With the large influx of raw sequence data from genome sequencing projects, there is a need for reliable automatic methods for protein sequence analysis and classification. The most useful tools use various methods for identifying motifs or domains found in previously characterized protein families. This article reviews the tools and resources available on the web for identifying signatures within proteins and discusses how they may be used in the analysis of new or unknown protein sequences.pmid:11806833 pmcid:PMC150457 fatcat:jqx7k7zk5jbe7pp3nrg22lo32e