Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Li, Weizhong; Godzik, Adam

doi:10.1093/bioinformatics/btl158

Cited by 9,356 publications

(7,220 citation statements)

References 4 publications

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“…The Swiss‐Prot and Pfam databases were used to identify the ORFs, and 107,242 transcripts (56.3% of total transcripts) were used to successfully predict ORFs with an average size of 196 amino acids and a N50 size of 314 amino acids. As the complement to TransDecoder, GeneMarkS‐T program (Tang et al., 2015) was used to predict ORFs, and 63,831 ORFs were obtained, after removing redundant ORFs determined by Cd‐hit package (Li & Godzik, 2006), 2,240 ORFs were added to TransDecoder prediction set, and finally 109,482 transcripts were successfully predicted ORFs. We then used several complementary routes to annotate the transcript sequences.…”

Section: Resultsmentioning

confidence: 99%

De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.

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Section: Resultsmentioning

confidence: 99%

De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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“…We set out to merge contigs derived from the same population into clusters representing population genomes. To this end, contig sequences were first clustered at 95% global average nucleotide identity (ANI) with cd-hit-est 58 (options -c 0.95 -G 1 -n 10 -mask NX, Supplementary Fig. 7B), resulting in 10,578,271 non-redundant genome fragments.…”

Section: Genome Binning and Re-assemblymentioning

confidence: 99%

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux

Brum

Dutilh

et al. 2016

Nature

687

885

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Tara Oceans CoordinatorsInternational audienceOcean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks

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“…These analyses, in addition, were performed on a non-redundant data set at 90% sequence identity cutoff. The clustering was done using a CD-hit program [13]. The highest resolution structure which contains a specific metal was chosen as the representative of each cluster for atom and amino acid profile analysis.…”

Section: Data Set Under Investigationmentioning

confidence: 99%

Data mining of metal ion environments present in protein structures

Zheng

Chruszcz

Lasota

et al. 2008

Journal of Inorganic Biochemistry

286

337

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Analysis of metal-protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal binding sites in protein structures determined by X-ray crystallography and deposited in the PDB shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium resolution structures from the PDB with those from very high resolution small-molecule structures in the Cambridge Structural Database (CSD). For high resolution protein structures, the distribution of metal-protein or metal-water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0 -2.5 Å) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found.

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Cited by 9,356 publications

References 4 publications

De novo assembly and characterization of the Hucho taimen transcriptome

De novo assembly and characterization of the Hucho taimen transcriptome

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Data mining of metal ion environments present in protein structures

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