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Sequence clustering
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<p>In <a href="/facts/Bioinformatics/D5x2L8ee">bioinformatics</a>, sequence clustering <a href="/facts/Algorithm/fnl5NmRt">algorithms</a> attempt to group <a href="/facts/Biological_sequence/VaN6MEYh">biological sequences</a> that are somehow related. The sequences can be either of <a href="/facts/Genomic/pVU3BGpL">genomic</a>, "<a href="/facts/Transcriptome/h6CC0sR5">transcriptomic</a>" (<a href="/facts/Expressed_sequence_tag/yS3x0IvH">ESTs</a>) or <a href="/facts/Protein/Jxmagu3E">protein</a> origin. For proteins, <a href="/facts/Homologous_sequence/mCIVStrA">homologous sequences</a> are typically grouped into <a href="/facts/Protein_family/EHt5xwCA">families</a>. For EST data, clustering is important to group sequences originating from the same <a href="/facts/Gene/e1swwPY6">gene</a> before the ESTs are <a href="/facts/Sequence_assembly/owEm30vn">assembled</a> to reconstruct the original <a href="/facts/MRNA/oUL6qxQn">mRNA</a>. </p><p>Some clustering algorithms use <a href="/facts/Single-linkage_clustering/suwgF2yb">single-linkage clustering</a>, constructing a <a href="/facts/Transitive_closure/HEtgYGM4">transitive closure</a> of sequences with a <a href="/facts/Sequence_similarity/mCIVStrA">similarity</a> over a particular threshold. UCLUST and CD-HIT use a <a href="/facts/Greedy_algorithm/alfsekco">greedy algorithm</a> that identifies a <a href="/facts/Representative_sequences/5GxucxDm">representative sequence</a> 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 <a href="/facts/Sequence_alignment/p8GQfF7b">sequence alignment</a>. Sequence clustering is often used to make a non-redundant set of <a href="/facts/Representative_sequences/5GxucxDm">representative sequences</a>. </p><p>Sequence clusters are often synonymous with (but not identical to) <a href="/facts/Protein_family/EHt5xwCA">protein families</a>. Determining a representative <a href="/facts/Tertiary_structure/VaN6MEYh">tertiary structure</a> for each sequence cluster is the aim of many <a href="/facts/Structural_genomics/njr8xKka">structural genomics</a> initiatives. </p>