Tag: MAFFT
Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis | BMC Infectious Diseases
Wu Z, McGoogan JM. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020;323(13):1239–42. Article CAS PubMed Google Scholar Kesheh MM, Hosseini P, Soltani S, Zandi M. An…
Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids | Virology Journal
Damiani AM, de Vries M, Reimers G, Winkler S, Osterrieder N. A severe equine herpesvirus type 1 (EHV-1) abortion outbreak caused by a neuropathogenic strain at a breeding farm in northern Germany. Vet Microbiol. 2014;172(3–4):555–62. Article PubMed Google Scholar Negussie H, Gizaw D, Tessema TS, Nauwynck HJ. Equine herpesvirus-1 myeloencephalopathy,…
Pairwise Alignment, Multiple Alignment, and BLAST
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef CAS PubMed Google Scholar Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database…
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article CAS PubMed Google…
Anopheles gambiae on remote islands in the Indian Ocean: origins and prospects for malaria elimination by genetic modification of extant populations
Irish, S. R., Kyalo, D., Snow, R. W. & Coetzee, M. Updated list of Anopheles species (Diptera: Culicidae) by country in the Afrotropical Region and associated islands. Zootaxa 4747(3), 401–449. doi.org/10.1646/zootaxa.4747.3.1 (2020). Article Google Scholar Jacques, B. Les moustiques de l’archipel Comores. Série Entomologie Médicale et Parasitologie 15(2), 153–170 (1977)….
Development and evaluation of specific polymerase chain reaction assays for detecting Theileria equi genotypes | Parasites & Vectors
Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS PubMed PubMed Central Google Scholar Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis
Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article PubMed Google Scholar Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article PubMed Google Scholar Amborella Genome Project et al. The Amborella…
The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking
Bacterial strains and growth conditions Veillonella parvula SKV38 was grown in SK medium (10 g/L tryptone [Difco], 10 g/L yeast extract [Difco], 0.4 g/L disodium phosphate, 2 g/L sodium chloride, and 10 ml/L 60% [wt/vol] sodium DL-lactate; described in ref. 51. Cultures were incubated at 37 °C in anaerobic conditions, either in anaerobic bags (GENbag anaero;…
Detection of a novel Babesia sp. in Amblyomma javanense, an ectoparasite of Sunda pangolins | Parasites & Vectors
Yabsley MJ, Shock BC. Natural history of zoonotic Babesia: role of wildlife reservoirs. Int J Parasitol Parasit Wildl. 2013;2:18–31. Article Google Scholar Hersh MH, Tibbetts M, Strauss M, Ostfeld RS, Keesing F. Reservoir competence of wildlife host species for Babesia microti. Emerg Infect Dis. 2012;18:1951–7. Article PubMed PubMed Central Google…
A DNA barcode library for woody plants in tropical and subtropical China
Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. Biological identifications through DNA barcodes. Proc Biol Sci 270, 313–321 (2003). Article CAS PubMed PubMed Central Google Scholar Huang, X., Ci, X., Conran, J. G. & Li, J. Application of DNA barcodes in Asian tropical trees –…
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article CAS PubMed Google Scholar Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article Google Scholar Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…
Chromosome-level genomes of three key Allium crops and their trait evolution
Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article Google Scholar Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….
The evolutionary innovation of root suberin lamellae contributed to the rise of seed plants
Fich, E. A., Segerson, N. A. & Rose, J. K. C. The plant polyester cutin: biosynthesis, structure, and biological roles. Annu. Rev. Plant Biol. 67, 207–233 (2016). Article CAS PubMed Google Scholar Geldner, N. The endodermis. Annu. Rev. Plant Biol. 64, 531–558 (2013). Article CAS PubMed Google Scholar Calvo-Polanco, M….
sequence alignment – I can’t make mafft run inside my program
This is easy because MAFFT is installed via Conda, but you have not activated that Conda environment, thus it will not give you access to the program. If you type … conda activate labinf mafft This will now work. To activate this inside a shell script you simply include the…
Single-cell transcriptomics reveals the brain evolution of web-building spiders
Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…
Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection
Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…
Dryad | Data — MtDNA genomes from Ranis individuals aligned with previously published ancient & modern humans
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups….
Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data
Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…
Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand
Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article PubMed PubMed Central Google Scholar Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article CAS PubMed PubMed Central Google…
Mycobacterium tuberculosis Sub Lineage 4.2.2/SIT149 as DR
Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…
Invasive Californian death caps develop mushrooms unisexually and bisexually
Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…
Identification and cultivation of anaerobic bacterial scavengers of dead cells
Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11. Article CAS PubMed PubMed Central Google Scholar Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. Production of refractory dissolved organic matter by bacteria. Science. 2001;292:917–20. Article CAS PubMed Google Scholar Liang…
Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales
Quesada A, Vincent WF. Strategies of adaptation by antarctic cyanobacteria to ultraviolet radiation. Eur J Phycol. 1997;32:335–42. Article Google Scholar Genuário DB, Corrêa DM, Komárek J, Fiore MF. Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol. 2013;49:1142–53. Article PubMed Google Scholar Makhalanyane TP, Valverde A, Gunnigle…
How To Install mafft on Debian 10
Learn how to install mafft on Debian 10 with this tutorial. mafft is Multiple alignment program for amino acid or nucleotide sequences Introduction In this tutorial we learn how to install mafft on Debian 10. What is mafft mafft is: MAFFT is a multiple sequence alignment program which offers three…
Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans
Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…
Index of /~psgendb/birchhomedir/local/pkg/ugene/data/cmdline
Name Last modified Size Description Parent Directory – align-clustalo.uwl 2019-09-24 01:05 3.0K align-clustalw.uwl 2019-09-24 01:05 5.1K align-kalign.uwl 2019-09-24 01:05 2.8K align-mafft.uwl 2019-09-24 01:05 2.7K align-tcoffee.uwl 2019-09-24 01:05 3.1K align-to-reference.uwl 2019-09-24 01:05 3.1K align.uwl 2019-09-24 01:05 2.7K convert-msa.uwl 2019-09-24 01:05 1.4K …
Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos
Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…
Generation of quality-controled SARS-CoV-2 variant stocks
World Health Organization. WHO Coronavirus (COVID-19) Dashboard. Available at covid19.who.int/ (2023). de Vries, M. et al. A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19. J. Virol. 95, e01819-20 (2021). Article PubMed PubMed Central Google Scholar FDA. Emergency Use Authorization (Eua) of…
Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle
Falkowski P. G., Raven J. A. Aquatic Photosynthesis (Princeton Univ. Press, 2013). Sanchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through earth history. Trends Microbiol. 30, 143–157 (2022). Article CAS PubMed Google Scholar Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol. 154,…
Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits
Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544. doi.org/10.1016/j.tree.2004.07.021 (2004). Article PubMed Google Scholar Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). Article ADS CAS PubMed …
Phylogenomics reveals the history of host use in mosquitoes
Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…
Permission error-hoc – User Support
kulandai1 (Balamurugan) October 5, 2023, 9:21am 1 HiI am running qiime in hpc with pbs script, I got error as Traceback (most recent call last):File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/q2cli/commands.py”, line 473, in callresults = action(**arguments)File “”, line 2, in align_to_tree_mafft_fasttreeFile “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py”, line 411, in parsl_wrappersetup_parallel()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”, line 69, in setup_parallelconfig_fp = _get_vendored_config()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”,…
Transposon-encoded nucleases use guide RNAs to promote their selfish spread
Siguier, P., Gourbeyre, E., Varani, A., Ton-Hoang, B. & Chandler, M. Everyman’s guide to bacterial insertion sequences. Microbiol. Spectr. 3, MDNA3-0030-2014 (2015). Article PubMed Google Scholar He, S. et al. The IS200/IS605 family and “peel and paste” single-strand transposition mechanism. Microbiol. Spectr. 3, MDNA3-0039-2014 (2015). Article ADS Google Scholar Kapitonov,…
Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago
Nutman, P. S. Centenary lecture. Phil. Trans. R. Soc. B 317, 69–106 (1987). Google Scholar Kelly, S., Radutoiu, S. & Stougaard, J. Legume LysM receptors mediate symbiotic and pathogenic signalling. Curr. Opin. Plant Biol. 39, 152–158 (2017). Article CAS PubMed Google Scholar Roy, S. et al. Celebrating 20 years of…
Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast
Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article CAS PubMed PubMed Central Google Scholar Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…
Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria
Ramanan R, Kim BH, Cho DH, Oh HM, Kim HS. Algae–bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv. 2016;34:14–29. Article CAS PubMed Google Scholar Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive earth’s biogeochemical cycles. Science. 2008;320:1034–9. Article CAS PubMed Google Scholar Buchan A, LeCleir GR,…
Characterization and organelle genome sequencing of Pyropia species from Myanmar
Yang, L. E. et al. Redefining Pyropia (Bangiales, Rhodophyta): Four new genera, resurrection of Porphyrella and description of Calidia pseudolobata sp. Nov. from China. J. Phycol. 56, 862–879 (2020). Article CAS PubMed Google Scholar Mumford Jr, T. F. Porphyra as Food: Cultivation and Economics in Algae and Human Affairs (ed….
Polish gulls harbor new coronavirus strains, spotlighting avian role in viral evolution
In a recent article published in the journal Scientific Reports, researchers characterize five strains of gammacoronaviruses (gCoV) and deltacoronaviruses (dCoV) that were detected in black-headed gulls (Chroicocephalus ridibundus) and common gulls (Larus canus) in Poland. Study: Gulls as a host for both gamma and deltacoronaviruses. Image Credit: Nataliya Dorokhina / Shutterstock.com Background The Orthocoronavirinae subfamily consists…
Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation
Cultivations and harvest Cupriavidus necator strain DSMZ 428 was grown in Ralstonia Minimal Media (RMM) with 100 mM HEPES pH 7.5 under chemostat conditions in a Photon Systems Instruments Multi-Cultivator MC-1000 OD. Each reactor tube was set up to a volume of 55 mL, OD600 0.05 and 3.5 g/L fructose. Once growth ceased,…
Error: Alpha rarefaction curve after merging the data of two different runs – Technical Support
Hi!I am facing a problem in alpha rarefaction curve plotting. In this study my samples were sequenced in two different runs “under same conditions” using Illumina Platform- MiSeq. For that reason I have merged the data from both the runs using same filtering parameters and following DADA2. Till “phylogeny align-to-tree-mafft-fasttree”…
Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
Brocks, J. J. et al. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578–581 (2017). Article ADS CAS PubMed Google Scholar Leliaert, F. Green algae: Chlorophyta and Streptophyta. In Encyclopedia of microbiology 457–468 (Academic Press, 2019). Zhang, Z. et al. Origin and evolution of…
One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade
Isolation and microscopy of Mantamonas sphyraenae sp. nov Mantamonas sphyraenae SRT-306 was collected on 26 Sep. 2013 from the surface of a barracuda caught in a lagoon on Iriomote Island, Taketomi, Okinawa Prefecture, Japan (24° 23′ 36.762″ N, 123° 45′ 22.572″ E). It was isolated manually from the rough sample…
Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing | BMC Infectious Diseases
Mboowa G, Sserwadda I, Bulafu D, Chaplain D, Wewedru I, Seni J, et al. Transmission Dynamics of Antimicrobial Resistance at a National Referral Hospital in Uganda. Am J Trop Med Hyg. 2021;105(2):498–506. Article CAS PubMed PubMed Central Google Scholar Rossolini GM, Arena F, Pecile P. Pollini SJCoip. Update on the…
Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409
Atanasov, A. G. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv. 33, 1582–1614 (2015). Article CAS PubMed PubMed Central Google Scholar Swamy, M. K. et al. Biotechnology of camptothecin production in Nothapodytes nimmoniana, Ophiorrhiza sp. and Camptotheca acuminata. Appl. Microbiol. Biotechnol. 105, 9089–9102…
What programs allow you to find the mutation rate of many sequences without needing to calculate by hand?
What programs allow you to find the mutation rate of many sequences without needing to calculate by hand? 0 Many methodologies require extensive calculation to determine mutation rate, but I am looking for a program (MAFFT, MEGA 11, BEAST, Arlequin, etc.) that has a feature that allows for the calculation…
Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade
Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013. Article CAS PubMed Google Scholar Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog. 2013;5:e23. Article Google Scholar Collins…
Regulation of gene editing using T-DNA concatenation
Gelvin, S. B. Integration of Agrobacterium T-DNA into the plant genome. Annu. Rev. Genet. 51, 195–217 (2017). Article CAS PubMed Google Scholar Gelvin, S. B. Plant DNA repair and Agrobacterium T-DNA integration. Int. J. Mol. Sci. doi.org/10.3390/ijms22168458 (2021). Jupe, F. et al. The complex architecture and epigenomic impact of plant…
Course on Phylogenomics
Dear all, We are excited to announce our upcoming online course on Phylogenomics, focused on Phylogenetic Inference and Divergence-Time Estimation with Genomic Data Sets. This course aims to provide researchers with the necessary tools and techniques to harness the power of genomic data for understanding evolutionary relationships and divergence times….
Interrogating the viral dark matter of the rumen ecosystem with a global virome database
Gregory, A. C. et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019). Article CAS PubMed PubMed Central Google Scholar Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016). Article CAS PubMed Google Scholar Camarillo-Guerrero, L….
Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization
Buettgens, M., Blavin, F. & Pan, C. The affordable care act reduced income inequality in the US. Health Aff. 40, 121–129 (2021). Article Google Scholar Chen, E. & Miller, G. E. Socioeconomic status and health: mediating and moderating factors. Annu. Rev. Clin. Psychol. 9, 723–749 (2013). Article PubMed Google Scholar …
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
Sample collection Previously, we collected nasal samples from WTD in northeastern Ohio focusing on metropolitan area parks11. In the present study, we expanded geographical study area by approximately 1000-fold to target the entire state of Ohio. We collected 1522 nasal swabs from WTD across 83 of Ohio’s 88 counties from…
Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis | Parasites & Vectors
Miterpáková M, Trbolová A, Hurníková Z, Balicka A, Čabanová V, Valentová D, et al. Thelazia callipaeda in Slovakia—from sporadic cases to endemic areas. Parasitol Int. 2022;87:102495. doi.org/10.1016/j.parint.2021.102495. Article PubMed Google Scholar Gama A, Pires I, Canado M, Coutinho T, Lopes AP, Latrofa MS, et al. First report of Thelazia callipaeda…
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article ADS CAS PubMed Google Scholar Porubsky, D. et al. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986–2005 (2022). Article …
Time-dependent variations in BK polyomavirus genome from kidney transplant recipients with persistent viremia
Garcia, G. G., Harden, P. & Chapman, J. The global role of kidney transplantation. Kidney Blood Press. Res. 35(5), 299–304 (2012). Article PubMed Google Scholar Tonelli, M. et al. Systematic review: Kidney transplantation compared with dialysis in clinically relevant outcomes. Am. J. Transplant. 11(10), 2093–2109 (2011). Article CAS PubMed Google…
Genome mining shows that retroviruses are pervasively invading vertebrate genomes
Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol 17, 355–370 (2019). Article CAS PubMed Google Scholar Stoye, J. P. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat. Rev. Microbiol 10, 395–406 (2012). Article CAS PubMed Google Scholar Zheng, J., Wei, Y. &…
Align raw Nanopore reads (amplicon, long PCR)
long PCR, 6000 bp, long indels (>100bp), multicopy gene = multiple amplicons from same PCR but only differ in indel meaning minimal substitutions: variance~1%, 2000 reads per sample, homopolymers (12bp) and tandem repeats (up to 55 fold, length 12-250bp), no reference available I want to de-noise my amplicons and generate…
Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle
Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article CAS PubMed PubMed Central Google Scholar Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…
Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing | BMC Infectious Diseases
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Comparative analysis of carbapenem-resistant K. pneumoniae
Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…
Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia | Parasites & Vectors
Zumpt F. Myiasis in man and animals in the old world. A textbook for physicians, veterinarians and zoologists. London: Butterworth; 1965. Google Scholar Stevens JR, Wall R. Genetic variation in populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences….
The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses | Parasites & Vectors
Cowie RH. Annotated catalogue of species of Angiostrongylus and the related genera Gallegostrongylus, Rodentocaulus and Stefanskostrongylus (Nematoda: Metastrongyloidea, Angiostrongylidae). J Helminthol. 2019;93:389–423. Article PubMed Google Scholar de Almeida LR, de Souza JGR, Santos HA, Torres EJL, Vilela R, do V, Cruz OMS, et al. Angiostrongylus minasensis n. sp.: new species…
Phylogenetic tree differ between including and excluding other species bacteria within same genus
Phylogenetic tree differ between including and excluding other species bacteria within same genus 0 Hello, I am new microbiology researcher currently researching bacteria using whole genome sequencing and currently doing analysis. I intend to create bacteria phylogenetic tree using BV-BRC services. The tree was succesfully created using MAFFT program with…
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria
Baumgartner, K., Coetzee, M. P. A. & Hoffmeister, D. Secrets of the subterranean pathosystem of Armillaria: subterranean pathosystem of Armillaria. Mol. Plant Pathol. 12, 515–534 (2011). Article PubMed PubMed Central Google Scholar Heinzelmann, R. et al. Latest advances and future perspectives in Armillaria research. Can. J. Plant. Pathol. 41, 1–23…
Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction
Simberloff, D. et al. Impacts of biological invasions: What’s what and the way forward. Trends Ecol. Evol. 28, 58–66 (2013). Article PubMed Google Scholar Bellard, C., Cassey, P. & Blackburn, T. M. Alien species as a driver of recent extinctions. Biol. Lett. doi.org/10.1098/rsbl.2015.0623 (2016). Article PubMed PubMed Central Google Scholar …
Multiple sequence aligment orientation
Multiple sequence aligment orientation 1 I’m seeking assistance with aligning multiple sequences using MAFFT. I’ve encountered a challenge as some of the sequences are on the forward strand, while others are on the reverse strand. I understand that for a successful multiple sequence alignment, all sequences need to have the…
Sample ID in feature table and meta data not in order – Other Bioinformatics Tools
A. I got this error (below) for this code physeq <- qza_to_phyloseq( features = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/dada2_table_16S.qza”, tree = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza”, taxonomy = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/taxonomy.qza”, metadata = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/metadata16S.tsv” )Error in validObject(.Object) : invalid class “phyloseq” object:Component sample names do not match.Try sample_names() As I was trying to look into detail, this was the error,…
Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm
Hernández-Sánchez, et al. LEAfing through literature: Late embryogenesis abundant proteins coming of age-achievements and perspectives. J. Exp. Bot. 73, 6525–6546 (2020). Article Google Scholar Graether, S. P. Proteins involved in plant dehydration protection: The late embryogenesis abundant family. Biomolecules 12, 1380 (2022). Article CAS PubMed PubMed Central Google Scholar Dure,…
Plugin error from phylogeny: Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’ returned non-zero exit status 1. – Technical Support
Hello, I am experiencing the following error (below) when running the following command (below). I tried this command on multiple cloud instances with high specs, and I have tried running the artifact on the latest version of QIIME 2 after initially trying this on version QIIME2_2019.10. I even tried filtering…
Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil
Mourad, O., Makhani, L. & Chen, L. H. Chikungunya: an emerging public health concern. Curr. Infect. Dis. Rep. 24, 217–228 (2022). Article PubMed PubMed Central Google Scholar Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: a review. Front. Public Health 9, 715759…
CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don)
Christenhusz, M. J. M. et al. A new classification and linear sequence of extant gymnosperms. Phytotaxa 19, 55–70 (2011). Article Google Scholar Forestry Agency. Statistical Handbook of Forest and Forestry. (Japan Forest Foundation, 2017) (in Japanese). Forestry Agency. Annual Report on Forest and Forestry in Japan. Fiscal Year 2018 (Summary)….
Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution
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Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs
Floudas, D. et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336, 1715–1719 (2012). Article ADS CAS PubMed Google Scholar Bissaro, B., Várnai, A., Røhr, Å. K. & Eijsink, V. G. H. Oxidoreductases and reactive oxygen species in conversion of lignocellulosic biomass. Microbiol. Mol…
A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)
Formenti, G. et al. The era of reference genomes in conservation genomics. Trends Ecol. Evol. 37, 197–202 (2022). Article CAS PubMed Google Scholar Lee, H. et al. Third-generation sequencing and the future of genomics. bioRxiv, 048603 (2016). Irestedt, M. et al. A guide to avian museomics: Insights gained from resequencing…
Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support
Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…
The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation
Billings, W. Adaptations and origins of alpine plants. Arct. Alp. Res. 6, 129–142 (1974). Article Google Scholar Agakhanjanz, O. & Breckle, W. Origin and evolution of the mountain flora in middle Asia and neighbouring mountain regions. in Arctic and Apine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds. Chapin, F. &…
Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs
Booth, B. C. & Marchant, H. J. Parmales, a new order of marine chrysophytes, with desriptions of three new genera and seven new species. J. Phycol. 23, 245–260 (1987). Article Google Scholar Ichinomiya, M. et al. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to…
Is it possible to get a pairwise distance matrix from a mafft alignment?
Is it possible to get a pairwise distance matrix from a mafft alignment? 1 I’ve googled around a bit. From reading the publications and software documentation, its clear that there is a distance matrix being used but it doesnt seem possible to obtain. There is rumor of a –distout flag…
Mitochondrial DNA is a target of HBV integration
Patients Tumour tissues from seven HBsAg-positive patients (6 men, 1 woman; mean age 66.7 ± 8 years) with HBV-related HCC and paired adjacent non-tumour tissues from six of them were studied. The clinical, histological, and virologic characteristics of the patients are summarised in Table 1. Two normal liver samples from HBV-negative patients who…
Parallel and convergent genomic changes underlie independent subterranean colonization across beetles
Conway Morris, S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 96, 1313–1337 (2009). Article ADS CAS PubMed Google Scholar Stern, D. L. The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764 (2013). Article CAS PubMed Google Scholar Christiansen, K. Convergence and parallelism in cave entomobryinae….
Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013). Article CAS PubMed PubMed Central Google Scholar Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013). Article CAS PubMed PubMed Central Google Scholar Zetsche, B. et al. Cpf1 is a single…
BTN3A3 evasion promotes the zoonotic potential of influenza A viruses
Lipsitch, M. et al. Viral factors in influenza pandemic risk assessment. eLife doi.org/10.7554/eLife.18491 (2016). Afrache, H., Gouret, P., Ainouche, S., Pontarotti, P. & Olive, D. The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response. Immunogenetics 64, 781–794 (2012). Article CAS PubMed Google Scholar Ye,…
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…
phylogenetics – Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average
I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of the codon sequences are at half length. If average is X then some sequences are X/2. This is choking IQ-Tree….
Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons
Clinical RNA SARS-CoV-2 isolate For surveillance studies, a set of residual nasopharyngeal swab specimens positive for SARS-CoV-2 qRT-PCR from the Republican Diagnostic Centre (RDC) (umc.org.kz/en/) and private laboratory KDL “Olymp” (www.kdlolymp.kz/) were collected across the Republic of Kazakhstan between 2020 and 2022. 341 sequences that passed quality control are deposited…
Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average.
Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average. 0 I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of…
MAFFT alignment options – User Guide to MegAlign Pro
The MAFFT algorithm is for gene level alignment of either protein or nucleotide sequences. If you want to align a large number of sequences in MegAlign Pro, we recommend using this algorithm. As of the Lasergene 17.3 release (August 2021), MegAlign Pro uses MAFFT7. This powerful aligner can typically align…
The genome of Acorus deciphers insights into early monocot evolution
Lughadha, E. N. et al. Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates. Phytotaxa 272, 82–88 (2016). Article Google Scholar Group, A. P. An update of the Angiosperm Phylogeny Group classification for…
Epistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence
Begier, E. et al. Epidemiology of invasive Escherichia coli infection and antibiotic resistance status among patients treated in US hospitals: 2009-2016. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 73, 565–574 (2021). Article CAS Google Scholar Bélanger, L. et al. Escherichia coli from animal reservoirs as a potential source of…
Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA
Uetz, P., Slavenko, A., Meiri, S. & Heinicke, M. P. Gecko diversity: A history of global discovery. Israel J. Ecol. Evol. 66, 117–125 (2020). Article Google Scholar Grismer, L. L. et al. Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its…
A complete telomere-to-telomere assembly of the maize genome
Dujon, B. The yeast genome project: what did we learn? Trends Genet. 12, 263–270 (1996). Article CAS PubMed Google Scholar Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000). Article PubMed Google Scholar Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering…
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). Article CAS PubMed Google Scholar Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). Article …
Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage
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Fine-scale genomic tracking of Ross River virus using nanopore sequencing | Parasites & Vectors
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Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data
Introduction Traditional Chinese herbal medicine plays an indispensable role in the treatment of multiple diseases in China and other developing countries (Newman et al., 2008). Apart from the traditional usage, many medicinal plants, such as Artemisia annua L. (artemisinin, Tu, 2016), Huperzia javanica (Sw.) C. Y. Yang (Huperzine A, Zangara, 2003;…
A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
Lederberg, J., Cavalli, L. L. & Lederberg, E. M. Sex compatibility in Escherichia Coli. Genetics 37, 720–730 (1952). Article CAS PubMed PubMed Central Google Scholar Elisabeth, G., Günther, M. & Manuel, E. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301 (2003). Article Google Scholar de la…
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 …
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
Johnson, W. E. Endogenous retroviruses in the genomics era. Annu. Rev. Virol. 2, 135–159 (2015). Article CAS PubMed Google Scholar Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol. 17, 355–370 (2019). Article CAS PubMed Google Scholar Johnson, W. E. Endless forms most viral. PLoS…
Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae)
Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…
Epidemiological inference for emerging viruses using segregating sites
Brief overview of inference approach Mutations occur during viral replication within infected individuals and these have the potential to be transmitted. During the epidemiological spread of an emerging virus or viral lineage, the virus population (distributed across infected individuals) thus accrues mutations and diversifies genetically. This joint process of viral…