Sequence clustering: Difference between revisions

Revision as of 20:22, 4 July 2008

Revision as of 13:53, 1 August 2008

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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 sequence|non-redundant]] set of [[representative sequences]].

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* [http://skyrah.bio.cc/RSDB/ RSDB: Representative Sequences DataBase project]

* [http://ratest.eng.uiowa.edu/pubsoft/clustering/ UICluster: Parallel Clustering of EST (Gene) Sequences]

* [http://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html BLASTClust single -linkage clustering with BLAST]

* [http://web.mit.edu/polz/clusterer Clusterer: extendable java application for sequence grouping and cluster analyses]

* [http://blast.wustl.edu/blast/README.html#Manifest PATDB: a program for rapidly identifying perfect substrings]