Sequence clustering

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In bioinformatics, sequence clustering algorithms attempt to group sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin. For proteins, homologous sequences are typically grouped into families. For EST data, clustering is important to group sequences originating from the same gene before the ESTs are assembled to reconstruct the original mRNA.

Generally, the clustering algorithms are single linkage clustering, constructing a transitive closure of sequences with a similarity over a particular threshold. The similarity score is often based on sequence alignment. Sequence clustering is often used to make a non-redundant set of representative sequences.

Sequence clusters are often synonymous with (but not identical to) protein families. Determining a representative tertiary structure for each sequence cluster is the aim of many structural genomics initiatives.

External links

Sequence clustering packages

Non-redundant sequence databases