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

Huang, Ying; Niu, Beifang; Gao, Ying; Fu, Li‐Chen; Li, Weizhong

doi:10.1093/bioinformatics/btq003

Cited by 2,213 publications

(1,697 citation statements)

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“…Assembled transcripts were aligned to our genome sequence using NCBI blastn v.2.2.30+ with an e-value cut-off of 1 × 10 −5 . Successfully aligned transcripts were clustered at 90% identity using CD-HIT (v. 4.5.4) 45 , with representative sequences from each cluster retained and used to help parameterize gene calling. Eighty-seven per cent of the trimmed RNA-seq reads aligned to the Oropetium genome, suggesting that the genome is largely complete (Supplementary Table 5).…”

Section: Methodsmentioning

confidence: 99%

“…Aligned and representative sequences from our transcriptome assembly were input to Maker as expressed sequence tag evidence. Rice and Brachypodium proteome sequences clustered at 90% identity using CD-HIT (v. 4.5.4) 45 with representative sequences from each cluster retained and input to Maker as multi-organismal protein homology evidence. The Oropetium repeat database was input to Maker as a custom repeat library.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

282

271

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Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly 1 . The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE) 2 . Here we report the whole-genome sequencing and assembly of the desiccationtolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.The genomes of Arabidopsis 3 , rice 4 , poplar, grape and Sorghum 5 were first sequenced using high-quality and reiterative Sanger-based approaches producing a series of 'gold standard' reference genomes. The advent of next-generation sequencing (NGS) technologies reduced costs of sequencing substantially, which has enabled sequencing of over 100 plant genomes 1 . The quality of plant genome assemblies depends on genome size, ploidy, heterozygosity and sequence coverage, but most NGS-based genomes have on the order of tens of thousands of short contigs distributed in thousands of scaffolds. The short read lengths of NGS, inherent biases and non-random sequencing errors have resulted in highly fragmented draft genome assemblies that are not complete, which means they are missing biologically meaningful sequences including entire genes, regulatory regions, transposable elements, centromeres, telomeres and haplotype-specific structural variations. It is becoming clear from ENCODE projects that complete genomes are needed to better understand the importance of the non-coding regions of genomes 2 .More than 40% of calories consumed by humans are derived from grasses, and the grass family (Poaceae) is arguably the most important plant family with regard to global food security 6 . The size and complexity of most grass genomes has challenged progress in gene discovery and comparative genomics, although draft genomes are now available for most agriculturally important grasses 1 . The largest genome assemblies, such as maize (2,300 megabases (Mb)) 7 , barley (5,100 Mb) 8 and wheat (hexaploid, 1...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

VanBuren

Bryant

Edger

et al. 2015

Nature

282

271

View full text Add to dashboard Cite

show abstract

“…Twenty-nine vertebrate proteomes were downloaded from GenBank (28 proteomes) and Ensembl (1 proteome). The CD-HIT algorithm was used to exclude redundant sequences in these proteomes (Huang et al, 2010). The orthologous proteins were screened out using the best reciprocal hit BLAST (version 2.2.28+) (Altschul et al, 1997).…”

Section: Evaluation Of the Foxp Subfamily Duplication Process Using Mmentioning

confidence: 99%

Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events

Song

Tang

Wang

2016

Gene

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“…In this regard, sequences with high genetic similarity (i.e. genetic distance < 5% (13) from each non-neighboring country were clustered using the Cluster Database at High Identity with Tolerance (CD-HIT) program (24), accessible via an online web server (25), and only one sequence per cluster was retained in each data set. Since the number of sequences from Iran and its neighboring countries was small, we did not reduce the number of these data.…”

Section: Hiv-1 Subtype B and Crf01_ae Data Setsmentioning

confidence: 99%

Spatio-Temporal Dynamics of HIV-I Subtype B and Circulating Recombinant Form 01_AE Clades in Iran: A Phylogeographic Approach

Eybpoosh

Bahrampour

Azadmanesh

et al. 2016

Iran Red Crescent Med J

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Background: The origins and spatio-temporal dynamics of the HIV-1 subtype B and CRF01_AE clades are largely unknown in Iran. Objectives: This study investigates the origins and spatio-temporal dynamics of HIV-1 subtype B and CRF01_AE clades in Iran using the most recent phylogeographic methods. Methods: This Bayesian phylogeographic study examined HIV-1 sequence data available in the Los Alamos HIV databases. For the purposes of this study, we retrieved all the eligible time-stamped and geo-referenced HIV-1 subtype B (pol p66 and p51 RT) and CRF01_-AE (gp160) sequences from Iran. The majority of these data were obtained from studies using convenience and snowball sampling. Evolutionary and phylogeographic parameters were jointly estimated for each clade using BEAST software v.1.8.1. A Bayesian stochastic search variable selection method, with a threshold of 3.0 for the Bayes factors test, was used to obtain significant migration rates of the virus. Results: Our results suggest that the subtype B epidemic was introduced to Iran from Southern China, Germany and the USA. Although the migration rate from the USA to Iran was found to be statistically insignificant, the results suggested that the USA was the earliest exporter of the subtype B to Iran (i.e. since 1974, 95% Highest Posterior Density (HPD) : 1966-1974). Moreover, based on our findings, the CRF01_AE clade was first introduced to Iran from Thailand (1988( , 95% HPD: 1986( -1990. Among the factors contributing to the transmission of subtype B to Iran from Germany is the transit of goods and long-distance truck driving. However, the factors behind the transmission of this clade from the USA and Southern China remain unknown. Similar to many countries, the introduction of CRF01_AE from Thailand might be attributed to sex tourism. Conclusions: There is evidence to suggest that subtype B and CRF01_AE were introduced to Iran through multiple pathways and origins, including Germany, Southern China, the USA, and Thailand. Factors such as international trade, the transit of goods, and tourism are among the most likely methods for transmission of these clades. However, the existing preventive strategies in Iran have been mostly focused on other risk groups, including sex workers and intravenous drug users. The findings of our study highlight the need for the further development of targeted preventive strategies, such as educational interventions, aimed at tourists, truck drivers, and people involved in international trade and transactions in order to prevent the onward transmission of disease.

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

Cited by 2,213 publications

References 9 publications

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events

Spatio-Temporal Dynamics of HIV-I Subtype B and Circulating Recombinant Form 01_AE Clades in Iran: A Phylogeographic Approach

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