Sequence clustering: Difference between revisions

Revision as of 17:54, 21 May 2004

Revision as of 04:40, 22 May 2004

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In [[bioinformatics]], '''sequence clustering''' [[algorithm]]s attempt to group

sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" ([[expressed sequence tag|ESTs]]) or [[protein]] origin.

For proteins, [[Homology (biology)|homologous]] sequences are typically grouped into [[protein family|families]]. For EST data, clustering is important to group sequences originating from the same [[gene]] before the ESTs are [[sequence assembly|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 sequencessequence|non-redundant]] set of sequences.

Sequence clustering is often used to make a [[Non redundant sequences|non-redundant]] set of sequences.

== External links ==

=== Sequence Clusteringclustering Packagespackages ===

* [http://www.ebi.ac.uk/~holm/nrdb90 RDB90 and nrdb90.pl: a nonredundant sequence database]

* [http://www.ebi.ac.uk/research/cgg/tribe/ TribeMCL: a method for clustering proteins into related groups]

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<!-- * [http://bio.cc/RSDB RSDB] broken link -->

=== Non-Redundantredundant Sequencesequence Databasesdatabases ===

* [http://www.fccc.edu/research/labs/dunbrack/pisces/ PISCES: A Protein Sequence Culling Server]