Tag: MAFFT
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,…
Impact of host age on viral and bacterial communities in a waterbird population
Woolhouse MEJ, Gowtage-Sequeria S. Host range and emerging and reemerging pathogens. Emerg Infect Dis. 2005;11:1842–7. Article PubMed PubMed Central Google Scholar Allen T, Murray KA, Zambrana-Torrelio C, Morse SS, Rondinini C, Di Marco M, et al. Global hotspots and correlates of emerging zoonotic diseases. Nat Commun. 2017;8:1–10. Article CAS Google…
Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora
Choo, L. M., Niissalo, M. A., Leong, P. K. F. & Khew, G. S. The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae). Phytotaxa 458, 159–166 (2020). Nguyet, H. N. L. et al. An updated checklist of Theaceae and a new species…
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.,…
Harrison’s rule corroborated for the body size of cleptoparasitic cuckoo bees (Hymenoptera: Apidae: Nomadinae) and their hosts
Fisher, D. O. & Dickman, C. R. Body size-prey size relationships in insectivorous marsupials: Tests of three hypotheses. Ecology 74, 1871–1883 (1993). Article Google Scholar Woodward, G. & Hildrew, A. G. Body-size determinants of niche overlap and intraguild predation within a complex food web. J. Anim. Ecol. 71, 1063–1074 (2002)….
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…
Tempo and drivers of plant diversification in the European mountain system
Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article Google Scholar Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS CAS PubMed Article Google…
MAFFT benchmark
Benchmark dataset The following datasets, HomFam and OXFam were used as benchamrk datasets in “Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees”. HomFam This HomFam dataset is modified version of original HomFam dataset constructed by the authors of Clustal…
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…
Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species
Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…
Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology
Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed Google Scholar Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed Google Scholar Rosenqvist G, Berglund A. Sexual signals and mating…
Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)
Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS CAS Article PubMed PubMed Central Google Scholar WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…
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…
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis
Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS PubMed Google Scholar Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…
Clustal Processing Massive Dataset
Hello wonderful beings of bioinformatics! I’m new to this world and could use some help. My job is to run multiple sequence alignment on a large dataset. I am looking into the L1 family of genes and wanting to compare 7,525 elements of full length sequences. Each sequence is ~6,000…
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…
Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea
1. Osellame, L. D., Blacker, T. S. & Duchen, M. R. Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metab. 26, 711–723 (2012). CAS PubMed PubMed Central Google Scholar 2. Bernt, M., Braband, A., Schierwater, B. & Stadler, P. F. Genetic aspects of mitochondrial genome evolution….
Long read de novo phylogenetic tree for metagenome
Long read de novo phylogenetic tree for metagenome 0 What tools are available to create de novo phylogenetic trees for long read metagenome datasets? phyloT seems to construct one based on taxonomy and NCBI/GTDb information rather than read alignment. Is MAFFT commonly used? What is the standard methodology? (For reference,…
Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium | BMC Biotechnology
1. Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, et al. Positive selection driving cytoplasmic genome evolution of the medicinally important ginseng plant genus Panax. Front Plant Sci. 2018;9:359. doi.org/10.3389/fpls.2018.00359. Article PubMed PubMed Central Google Scholar 2. Takeshi T, Marouane B, Takuya I, Kazusato O, Kimiko…
Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support
Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…
Aligning large sets of sequences
Hello folks, I am seeking an advice on Multiple Sequence Alignment that I am trying to get. The fasta file i am trying to align belongs to Sars-Cov-2 Spike protein, it has nearly 600k sequences and ranges from 1270-1275 aa. I have aligned with clustalo and mafft with default parameters….
GitHub – sdellicour/sars-cov-2_liege
This repo gathers all the input files and scripts related to our study entitled “Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020” (Bollen et al. submitted): R scripts to prepare, analyse, and visualise the phylogeographic analyses performed in this study, Geographic Information…
Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020
1. Dudas, G. et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544, 309–315 (2017). ADS CAS Article Google Scholar 2. Kafetzopoulou, L. E. et al. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 363, 74–77 (2019). ADS CAS Article …
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…
Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis
1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS PubMed PubMed Central Article Google Scholar 2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed Article PubMed Central Google Scholar 3. Borrel G, McCann A, Deane J, Neto…
Aligning multiple overlapping DNA sequence reads to predicted sequence not working
Aligning multiple overlapping DNA sequence reads to predicted sequence not working 0 Hi All, I work on a large protein (5 subunits, 5850 bp) that I have to sequence using multiple Sanger Sequence reactions (usually ~10). I want to be able to get the sequencing results and align them to…
Genome of a middle Holocene hunter-gatherer from Wallacea
1. McColl, H. et al. The prehistoric peopling of Southeast Asia. Science 361, 88–92 (2018). CAS PubMed Article ADS Google Scholar 2. Hasanuddin. Gua Panningnge di Mallawa, Maros: kajian tentang gua hunian berdasarkan artefak batu dan sisa fauna. Naditira Widya 11, 81–96 (2017). Article Google Scholar 3. Bulbeck, D., Pasqua,…
How to split big .faa file into smaller .faa files
How to split big .faa file into smaller .faa files 1 I have a 10 gb .faa proteomes file that I want to run MAFFT on. But it is too big and hence I need to divide the file. How do I convert it to smaller files in windows without…
