CD-HIT Suite: a web server for clustering and comparing biological sequences

By Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li. 2010

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2014, methodology): “Various software platforms, including mothur (Schloss et al. , 2009), QIIME (Caporaso et al. , 2010), CD-HIT Suite (Huang et al. , 2010) and VAMPS (Huse et al. , 2014), have adopted most of these OTU identification strategies.”
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data (2013, methodology): “…each sequence read by its barcode, followed by similarity clustering to define operational taxonomic units (OTUs, sometimes referred to as taxa ) [9,10] can be performed by publicly available packages/pipelines, including QIIME [11], mothur [12], and PANGEA [13]; as well as virtual machine (VM)…”
US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes (2022, methodology): “Instead, incremental clustering was found by previous studies 8 to be the most efficient approach in such scenarios.”
Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors (2019, methodology): “The 131 predicted candidates were further clustered in CD-HIT to filter out similar peptides (> 0.85 sequence identity cut-off) (Huang et al., 2010).”
High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder (2015, unknown): “%) similarity by clustering with CD-HIT as described above.”
Oxygenic photosynthesis as a protection mechanism for cyanobacteria against iron-encrustation in environments with high Fe2+ concentrations (2014, methodology): “Clustering of the sequences at 98% similarity cutoff using the CDHIT-EST software(Huang et al., 2010; Fu et al., 2012) supports the phylogenetic tree and shows that no overlap is found between sequences from the Fe2+-poor and the Fe2+-rich reactors.”
Heterotrophic bacteria as major nitrogen fixers in the euphotic zone of the Indian Ocean (2014, methodology): “Clones with 100% amino acid sequence similarity were assigned to the same representative type using the CD-HIT suite [Huang et al., 2010].”
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands (2013, methodology): “Small molecule ligands with similar structures were clustered using Pipeline Pilot (Accelrys, San Diego, CA, USA) and peptides with similar sequences were clustered using h-cd-hit, part of the CD-HIT Suite (27).”
New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A (2016, methodology): “(2014) using CD-HIT-EST or CD-HIT-EST-2D (Huang et al. 2010) at 90% nt similarity.”