Sequence clustering

In bioinformatics, sequence clustering algorithms attempt to group biological 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.

Some clustering algorithms use single-linkage clustering, constructing a transitive closure of sequences with a similarity over a particular threshold. UCLUST^[1] and CD-HIT^[2] use a greedy algorithm that identifies a representative sequence for each cluster and assigns a new sequence to that cluster if it is sufficiently similar to the representative; if a sequence is not matched then it becomes the representative sequence for a new cluster. 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.

Sequence clustering algorithms and packages

OrthoFinder:^[3] a fast, scalable and accurate method for clustering proteins into gene families (orthogroups)^[4]
UCLUST in USEARCH^[1]
CD-HIT^[2]
nrdb90.pl^[5]
TribeMCL: a method for clustering proteins into related groups^[6]
BAG: a graph theoretic sequence clustering algorithm^[7]
JESAM:^[8] Open source parallel scalable DNA alignment engine with optional clustering software component
UICluster:^[9] Parallel Clustering of EST (Gene) Sequences
BLASTClust single-linkage clustering with BLAST^[10]
(Multi)netclust:^[11] fast and memory-efficient detection of connected clusters in (multi-parametric) data networks^[12]
Clusterer:^[13] extendable java application for sequence grouping and cluster analyses
PATDB: a program for rapidly identifying perfect substrings
nrdb:^[14] a program for merging trivially redundant (identical) sequences
CluSTr:^[15] A single-linkage protein sequence clustering database from Smith-Waterman sequence similarities; covers over 7 mln sequences including UniProt and IPI
ICAtools^[16] - original (ancient) DNA clustering package with many algorithms useful for artifact discovery or EST clustering
Virus Orthologous Clusters:^[17] A viral protein sequence clustering database; contains all predicted genes from eleven virus families organized into ortholog groups by BLASTP similarity
Skipredudant EMBOSS tool^[18] to remove redundant sequences from a set