Tag: trimAL
Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor
Mandáková, T. & Lysak, M. A. Post-polyploid diploidization and diversification through dysploid changes. Curr. Opin. Plant Biol. 42, 55–65 (2018). Article PubMed Google Scholar Blanc, G. & Wolfe, K. H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678 (2004). Article CAS …
Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution
Manrique, P., Dills, M. & Young, M. J. The human gut phage community and its implications for health and disease. Viruses 9, 141 (2017). Article PubMed PubMed Central Google Scholar Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J….
Biochemical and genotyping analyses of camels (Camelus dromedaries) trypanosomiasis in North Africa
Igbokwe, I. O. Evolving anti-disease strategies from biochemical pathogenesis of African trypanosomiasis. Adv. Cytol. Pathol. 3(2), 33–39 (2018). Google Scholar Njiru, Z. K., Constantine, C. C., Gitonga, P. K., Thompson, R. C. & Reid, S. A. Genetic variability of Trypanosoma evansi isolates detected by inter-simple sequence repeat anchored-PCR and microsatellite….
Assessing the biogeography of marine giant viruses in four oceanic transects
Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020;84:e00061–19. Article CAS PubMed PubMed Central Google Scholar Wilhelm S, Bird J, Bonifer K, Calfee B, Chen T, Coy S, et al. A…
Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles
Feldhaar H. Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol. 2011;36:533–43. Article Google Scholar Douglas AE. Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb Perspect Biol. 2014;6:a016113–a016113. Article PubMed PubMed Central Google Scholar Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive…
Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes
Reconstruction of gene and macro-synteny trees for the three studied Papaver species Syntenic blocks within the three Papaver species were identified with OrthoFinder v2.3.15. Orthologous and paralogous relationships, as well as orthogroups, were inferred using the parameters “-M msa -T fasttree” based on proteome sequences from multiple species. The resulting…
Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature 2015;528:504. Article CAS PubMed PubMed Central Google Scholar van Kessel MA, Speth DR, Albertsen M, Nielsen PH, den Camp HJO, Kartal B, et al. Complete nitrification by a single microorganism….
An ancient metalloenzyme evolves through metal preference modulation
Jayaraman, V., Toledo-Patino, S., Noda-Garcia, L. & Laurino, P. Mechanisms of protein evolution. Protein Sci. 31, e4362 (2022). Article CAS PubMed Google Scholar Huang, R. et al. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc. Natl Acad. Sci. USA 109, 2966–2971 (2012). Article CAS PubMed PubMed Central …
Ranjit Naiknavare elected as new President of CREDAI Pune Metro
Pune builder Ranjit Naiknavare has been elected unopposed as the president of the Pune division of the Confederation of Real Estate Developers Associations of India (CREDAI) Pune Metro. The CREDAI is the apex body for private Real Estate developers in India. In the recently held meeting of the managing committee,…
Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments
Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Planet. Sci. 48, 205–231 (2020). Article CAS Google Scholar Feng, D. et al. Cold seep systems in the South China Sea: An overview. J. Asian Earth SCI 168, 3–16 (2018). Article Google Scholar Dubilier, N., Bergin, C….
Identification and gene expression analysis of serine proteases and their homologs in the Asian corn borer Ostrinia furnacalis
Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003). Article CAS PubMed Google Scholar Rawlings, N. D. & Barrett, A. J. Evolutionary families of peptidases. Biochem….
Safety Week at CREDAI Pune Metro
Guests emphasise on better facilities; children of construction workers present a play on child rights CREDAI Pune Metro celebrated National Safety Week 2023 at multiple construction sites in Pune and Pimpri-Chinchwad. An event was organised by Panchashil at East Side Business Park in Kalyani Nagar. Additional labour commissioner Shailendra Pol,…
A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans | BMC Biology
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article CAS PubMed PubMed Central Google Scholar Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…
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…
SESSION 4: Gene Trees – HackMD
SESSION 4: Gene Trees – HackMD ###### tags: `BOT3404` # SESSION 4: Gene Trees SESSION 4: Gene Tree [TOC] In this session we will be using the sequences retrieved from Session 3 and running a few commands to be able to arrange the sequences into a gene tree. ### MAFFT…
Magicbricks Leadership Dialogue brings together industry leaders to discuss real estate growth
NL Corresspondent Jammu Tawi: The real estate market in India has recovered steadily in 2022 with growing residential and commercial demand, complemented by the gradual reopening of offices and educational institutions. The COVID-19 pandemic had severely impacted the real estate sector, leading to slowdown in sales, delays in project…
Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids
Orcutt B, D’Angelo T, Jungbluth SP, Huber JA, Sylvan JB. Microbial life in oceanic crust. OSF Preprints, 2020; doi.org/10.31219/osf.io/2wxe6. Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci. 2009;1178:47–64. Nigro OD, Jungbluth SP, Lin HT, Hsieh CC, Miranda JA, Schvarcz CR, et…
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…
Paris Gilton closed the fashion show at the extravagant spring cloth
Peris Gilton took part in the Milan fashion fashion as a model. But more, she shrugged off the show in the image of the intended one, which is the most prestigious exit of the show. The first ce bula was named unconventionally. Legendary bіlyavka, specialization of the crazy glamor of…
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….
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes
Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS PubMed Google Scholar Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed PubMed…
Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species
Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS Google Scholar Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS PubMed Google…
Change Residue Output Length in trimAl?
Change Residue Output Length in trimAl? 0 Hello, I am looking for a way to change the length of the residues printed in the output of trimAl. Using clustalo, I have generated .aln data that looks like so: chr1_38402816-38409352 ———————————————————————————agatcatgaacttttgctc–ca—agaactattgcaggaa-cataccagga-aagccgagagaatccacagaccctttgaaggaagtggatt chr1_41176265-41182362 ——————————————————————————————————————————————————————————- chr1_42059276-42065372 ——————————————————————————————————————————————————————————- I was able to see 175…
DOWNLOAD: Trimal .Mp4 & MP3, 3gp
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Trimal – Names and nicknames style for Trimal
We have almost all kind of nicknames like Free Fire nicknames, Arena of Valor nicknames (Liên Quân Mobile), Mobile Legends nicknames, PlayerUnknown’s Battlegrounds nicknames, PUBG nicknames, League of Legends: Wild Rift nicknames (Liên Minh Huyền Thoại: Tốc Chiến), League of Legends nicknames (Liên Minh Huyền Thoại), Dota 2 nicknames, Love…
Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)
1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed Google Scholar 2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS PubMed PubMed Central Google Scholar 3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…
