Tag: CD-HIT
Backcrossing to different parents produced two distinct hybrid species
Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma 12:246. doi.org/10.1186/1471-2105-12-246 Article Google Scholar Anderegg WRL, Flint A, Huang C-Y, Flint L, Berry JA, Davis FW et al. (2015) Tree mortality predicted from drought-induced vascular damage. Nat Geosci 8:367–371 Article CAS Google Scholar …
A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters
Revsbech, N. P. et al. Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnol. Oceanogr.: Methods. 7, 371-381. (2009). Wright, J. J., Konwar, K. M. & Hallam, S. J. Microbial ecology of expanding oxygen minimum zones. Nat. Rev. Microbiol. 10, 381–394 (2012). Article CAS PubMed …
Prediction of protein subplastid localization and origin with PlastoGram
Data sets To create data sets of sequences corresponding to compartments of photosynthetic plastids, we searched the UniProt database for proteins annotated as localized in the chloroplast. Importantly, the UniProt keyword ’Chloroplast’ includes not only chloroplasts of green algae and land plants but also plastids of Rhodophyta, haptophytes and the…
Bowtie2 alignment on metagenomics – sum same sequence
Bowtie2 alignment on metagenomics – sum same sequence 0 Hello, I have multiple metagenomic assemblies. I have obtained the ffn file of the orfs, then merged them together and clustered them using cd-hit-est. when I use bowtie2 to map these sequences against reads, bowtie2 records multiple mappings (as it should)…
A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). Article CAS PubMed PubMed Central Google Scholar Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013)….
Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons
de La Torre, S., Snowdon, C. T. & Bejarano, M. Effects of human activities on wild pygmy marmosets in Ecuadorian Amazonia. Biol. Conserv. 94, 153–163 (2000). Article Google Scholar Turvey, S. T. & Crees, J. J. Extinction in the Anthropocene. Curr. Biol. 29, R982–R986 (2019). Article CAS PubMed Google Scholar …
Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)
Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article CAS PubMed Google Scholar Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….
Mirusviruses link herpesviruses to giant viruses
Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article CAS PubMed PubMed Central Google Scholar Suttle, C. A. Marine viruses — major players in the global…
Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes
Blume-Werry G, Krab EJ, Olofsson J, Sundqvist MK, Väisänen M, Klaminder J. Invasive earthworms unlock arctic plant nitrogen limitation. Nat Commun. 2020;11:1766. Article CAS PubMed PubMed Central Google Scholar Xing Y, Meng X, Wang L, Zhang J, Wu Z, Gong X, et al. Effects of benzotriazole on copper accumulation and…
Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling
Ahsan, D. A., Naser, M. N., Bhaumik, U., Hazra, S. & Bhattacharya, S. B. Migration, Spawning Patterns and Conservation of Hilsa Shad (Tenualosa ilisha) in Bangladesh and India. Publ. by Acad. Found. India, New Delhi Int. Union Conserv. Nat. Nat. Resour. 95 (2014). De, D. et al. Nutritional profiling of…
Sensory specializations drive octopus and squid behaviour
van Giesen, L., Kilian, P. B., Allard, C. A. H. & Bellono, N. W. Molecular basis of chemotactile sensation in octopus. Cell 183, 594–604.e14 (2020). Article PubMed PubMed Central Google Scholar Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134 (2021)….
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article CAS PubMed Google Scholar Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…
CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts
Suttle, C. A. Environmental microbiology: Viral diversity on the global stage. Nat. Microbiol. 1, 16205 (2016). Article CAS PubMed Google Scholar Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020). Article ADS CAS PubMed PubMed Central Google Scholar Dutilh, B. E., Reyes,…
Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods | Environmental Microbiome
O’Neill J. The Review on Antimicrobial Resistance—tackling drug-resistant infections globally: final report and recommendations. 2016. Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet. 2022;399:629–55. Article CAS Google Scholar Laxminarayan R….
Toxins | Free Full-Text | Metagenome Analysis Identifies Microbial Shifts upon Deoxynivalenol Exposure and Post-Exposure Recovery in the Mouse Gut
1. Introduction Fusarium fungi are world-wide producers of a range of mycotoxins. Deoxynivalenol (DON) belonging to the group B trichothecenes, is one of the most prevalent food-associated mycotoxins mainly produced by Fusarium graminearum and Fusarium culmorum, and frequently contaminates cereals and cereal products [1,2]. Almost half of a total of…
Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007). Article CAS PubMed PubMed Central Google Scholar Glöckner, J. et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12, 1218–1229…
Big BCV (Biological Coefficient of Variation)
Big BCV (Biological Coefficient of Variation) – no sense to continue the analysis of differential gene expression? 2 Is it possible to perform differential gene expression analysis on data with such dispersion, BCV and MDSplot? (Fig. A, B) y_disp_design <- estimateDisp(y_filtered, design = design) y_disp_design$common.dispersion 0.3251901 Is it possible to…
SCRAPT: an iterative algorithm for clustering large 16S rRNA gene data sets
doi: 10.1093/nar/gkad158. Online ahead of print. Affiliations Expand Affiliations 1 Department of Computer Science, University of Maryland, College Park, 20742 MD, USA. 2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. Item in Clipboard Tu Luan et al. Nucleic Acids Res. 2023. Show details Display options Display…
Gene presence and absence analysis
Pangenome: Gene presence and absence analysis 1 Hello. I would like to have an idea for gene presence and absence determination for pangenome analysis. I have built a pangenome from several yeast strains of interest by merging each CDS and eliminate the redundantly using CD-HIT. Then, I mapped Illumina reads…
A bivalent remipede toxin promotes calcium release via ryanodine receptor activation
Recombinant peptide production Recombinant expression of Xt3a, Xt3a-D1, Xt3a-D2 and IpTxA was performed using an E. coli expression system. A gene encoding the peptide was subcloned into an expression vector containing a coding region with poly-histidine purification tag as well as a solubility tag (MBP for Xt3a and SUMO for…
A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics | Environmental Microbiome
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter nature. Nat Publ Group. 2013;499:431–7. CAS Google Scholar Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across…
Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars
Zhang J, Liu Y, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84. Article CAS PubMed Google Scholar Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots:…
Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains
This research complies with all relevant ethical regulations approved by the Human Investigation Review Board of Albert Szent-Györgyi Clinical Centre of the University of Szeged and the National Biodiversity Authority (NBA) of India. Permission for the faecal sample collection was obtained from the Human Investigation Review Board of Albert Szent-Györgyi…
Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut
Animal studies Animal care and study protocols were approved by the AAALAC-accredited Institutional Animal Care and Use Committee of the College of Agricultural Life Sciences at the University of Wisconsin-Madison (UW-Madison). All experiments with mice were performed under protocols approved by the UW-Madison Animal Care and Use Committee (Protocol number…
Bioinformatics Analysis of Viral Metagenomic Sequencing
Viral metagenomics is the study of viruses in environmental and biological samples by utilizing next generation sequencing that generates very large data sets. Viral metagenomics analyzes viral sequences to deduce the impact of viruses on the environment of human health. Unlike amplicon sequencing, metagenomics obtains and investigates genetic material directly…
Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga
Koonin, E. V. & Dolja, V. V. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014). Article CAS Google Scholar Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and…
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article CAS PubMed PubMed Central Google Scholar Ayala, J. A., Garrido, T., De Pedro,…
The evolutionary origin of host association in the Rickettsiales
Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS PubMed Article Google Scholar Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS PubMed PubMed Central Article Google Scholar Strassert, J. F. H.,…
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS PubMed Article Google Scholar Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….
minimum number of protein sequences for a sequence logo
minimum number of protein sequences for a sequence logo 1 Hi, I’m interested in generating sequence logo of a series of defensin related proteins I’ve clustered using CD-Hit. There are aproximately 7600 sequences with about 2500 clusters, but many of them have few sequences per cluster. Which is the minimum…
Index of /~psgendb/doc/pkg/cd-hit-v4.8.1-2019-0228/doc
Name Last modified Size Description Parent Directory – Figure1.png 2015-05-05 00:44 43K Figure2.png 2015-05-05 00:44 42K Figure3.png 2015-05-05 00:44 129K Figure4.png 2015-05-05 00:44 30K cd-hit-est.man 2020-06-16 12:13 5.6K cd-hit-otu-miseq-Fig..> 2017-03-25 12:00 117K cd-hit.man 2020-06-16 12:12 4.4K cdhit-user-guide.pdf 2017-05-01 11:52 412K …
Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis
1. Parte, A. C. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 42, D613-616 (2014). CAS PubMed Google Scholar 2. Krzyściak, W., Pluskwa, K. K., Jurczak, A. & Kościelniak, D. The pathogenicity of the Streptococcus genus. Eur. J. Clin. Microbiol. Infect. Dis. 32, 1361–1376 (2013). PubMed PubMed…
Petabase-scale sequence alignment catalyses viral discovery
Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…
Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet
1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS PubMed PubMed Central Google Scholar 2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS PubMed Google Scholar 3. Oh, J. et al. Temporal stability…
How to remove redundant sequences from fasta file ?
How to remove redundant sequences from fasta file ? 0 I’ve fasta file containing nucleotide sequences. How can I remove the redundant sequences?I’m trying to access cd-hit but web server is not available. Is there any other tool available for removing redundancy? I really appreciate any help or suggestion! redundant…
How to get a profile of consistent cd-hit clusters across different sequence files?
How to get a profile of consistent cd-hit clusters across different sequence files? 0 I have 10 different nucleotide sequence fasta files. I would like to run cd-hit on them and get a cluster abundance profile. If I run the fasta files on cd-hit separately, the clusters will not be…
