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Tag: K-mer
A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…
Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome
Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article ADS CAS PubMed Google Scholar Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…
MetaSPAdes genome assembly (shotgun metagenome singleend) – usegalaxy.org support
Busrak December 11, 2023, 3:31pm 1 Hi friends, Metagenomic single end raw data with cut adapt‘Maximum error rate 0.3’Match times: 1Minimum overlap length:3minimum lenght: 15Max N: 0.3Max expected errors: 30 parameters.Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes…
Origin and evolution of the triploid cultivated banana genome
Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS PubMed PubMed Central Google Scholar Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…
A CNN based m5c RNA methylation predictor
Hammad, M. et al. A novel end-to-end deep learning approach for cancer detection based on microscopic medical images. Biocybern. Biomed. Eng. 42(3), 737–748 (2022). Article Google Scholar Hammad, M. et al. Efficient multimodal deep-learning-based covid-19 diagnostic system for noisy and corrupted images. J. King Saud Univ.-Sci. 34(3), 101898 (2022). Article …
FIGURE S6. from Mitochondrial replication’s role in vertebrate mtDNA strand asymmetry
figure posted on 2023-12-08, 07:46 authored by André Gomes-dos-Santos, Nair Vilas-Arrondo, André M. Machado, Esther Román-Marcote, Jose Luís Del Río Iglesias, Francisco Baldó, Montse Pérez, Miguel M. Fonseca, L. Filipe C. Castro, Elsa Froufe GenomeScope2 k-mer (21) distributions displaying estimation of genome size (len), homozygosity (aa), heterozygosity (ab), mean k-mer…
finished abnormally, OS return value: 21
SPAdes error: finished abnormally, OS return value: 21 1 I’m having trouble using SPAdes. I’m using SPAdes to do paired end data assembly and I’m getting an unusual stop. error code: finished abnormally, OS return value: 21 Do you know how to resolve this issue? Environment: conda, SPAdes genome assembler…
Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph
Profiling metagenomes against databases allows for the detection and quantification of microbes, even at low abundances where assembly is not possible. We introduce sylph, a metagenome profiler that estimates metagenome-genome average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Sylph is the most accurate method on…
Evan Eichler, Long Read Sequencing of Complex Genomes | by Axial | Nov, 2023
Axial: linktr.ee/axialxyz Axial partners with great founders and inventors. We invest in early-stage life sciences companies such as Appia Bio, Seranova Bio, Delix Therapeutics, Simcha Therapeutics, among others often when they are no more than an idea. We are fanatical about helping the rare inventor who is compelled to build…
Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding
Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…
Uncertainty of how to proceed with Metagenomic Analysis of WGS data
Uncertainty of how to proceed with Metagenomic Analysis of WGS data 1 Hello guys, I am relatively new to metagenomic data analysis and even bioinformatics in general. To maybe give you a brief idea of what my issue is, I will just explain what my data is about: the data…
A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo
Animal models All procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) at Washington University in St. Louis, MO. Veterinary care and housing was provided by the veterinarians and veterinary technicians of Washington University School of Medicine under Dougherty lab’s approved IACUC protocol. All protocols…
Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article PubMed Google Scholar Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…
Estimate Genome Size
Estimate Genome Size 0 I would like to estimate genome size using the popular tutorial on Jellyfish provided here. However, I only have RNA-seq data with high coverage. Is it possible to utilize this type of data to achieve my goal?” jellyfish genome k-mer • 77 views Login before adding…
Spark-Based Label Diffusion and Label Selection Community Detection Algorithm for Metagenome Sequence Clustering
PLDLS, a parallel community detection algorithm in the spark framework, is designed to address the randomness of label selection during clustering and improve the completeness of metagenome sequence clustering. The algorithm combines four steps of node scoring and core node selection, core node diffusion and fast label selection, improved label…
Detection and characterization of putative hypervirulent Klebsiella pneumoniae isolates in microbiological diagnostics
Navon-Venezia, S., Kondratyeva, K. & Carattoli, A. Klebsiella pneumoniae: A major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol. Rev. 41(3), 252–275 (2017). Article CAS PubMed Google Scholar Marr, C. M. & Russo, T. A. Hypervirulent Klebsiella pneumoniae: A new public health threat. Expert Rev. Anti Infect. Ther. 17(2),…
Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]
Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…
Exploratory Data Analysis and Prediction of Human Genetic Disorder and Species Using DNA Sequencing
Sanders, S.J.: First glimpses of the neurobiology of autism spectrum disorder. Curr. Opin. Genet. Dev. 33, 80–92 (2015) CrossRef Google Scholar Schizophrenia working group of the psychiatric genomics consortium: biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014) Google Scholar Jamie, P., et al.: Global, regional, and national…
Best way to use k-mers as a predictor in my neural network
Best way to use k-mers as a predictor in my neural network 1 I have my genome as well as some predictors (eg chromosome, GC content, etc) for a response variable, for each window of the genome. I’m working in TensorFlow. I also want to use the k-mers or maybe…
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…
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Compagno, L. J. V. Alternative life-history styles of cartilaginous fishes in time and space. Environ. Biol. Fishes 28, 33–75 (1990). Article Google Scholar Kriwet, J., Witzmann, F., Klug, S. & Heidtke, U. H. J. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proc. Biol. Sci….
checkstrand tool (from BBMap suite) question
checkstrand tool (from BBMap suite) question 0 Brian Bushnell : I was looking at checkstrand.sh application included in the latest version of BBMap. While running a test analysis using a human sample I noticed that the output for the tool was identical in following two scenarios using a single end…
Integration of phenotypic, qPCR and genome sequencing methodologies for the detection of antimicrobial resistance and virulence in clinical isolates of a tertiary hospital, India
Azimi A, Peymani A, Pour PK (2018) Phenotypic and molecular detection of metallo-β-lactamase-producing Pseudomonas aeruginosa isolates from patients with burns in Tehran. Iran Rev Soc Bras Med Tro 51:610–615. doi.org/10.1590/0037-8682-0174-2017 Article Google Scholar Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology….
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples
Tuganbaev, T. et al. Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis. Cell 182, 1441–1459 (2020). Article CAS PubMed Google Scholar Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592–597 (2018). Article CAS PubMed PubMed Central Google Scholar Bullman,…
Kallisto abundance.tsv
Kallisto abundance.tsv 1 Hello, I am running Kallisto for the first time and I am wondering if I am executing the correct command. I am adding six samples but in the end it only generates an abundance.tsv file that does not contain columns corresponding to the samples I entered. Is…
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…
plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style | BMC Genomics
Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990;18(20):6097–100. Article CAS PubMed PubMed Central Google Scholar Colaert N, Helsens K, Martens L, Vandekerckhove J, Gevaert K. Improved visualization of protein consensus sequences by iceLogo. Nat Methods. 2009;6(11):786–7. Article CAS PubMed Google Scholar …
Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits
Swingle, W. T. & Reece, P. C. In The Citrus Industry, History, World Distribution, Botany, and Varieties, Vol. 1 (eds Reuther, W. et al.) 190–143 (Univ. of California Press, 1967). Morton, C. M. & Telmer, C. New subfamily classification for the Rutaceae. Ann. Mo. Bot. Gard. 99, 620–641 (2014). Article …
Challenges and opportunities in sharing microbiome data and analyses
Kyrpides, N. C., Eloe-Fadrosh, E. A. & Ivanova, N. N. Microbiome data science: understanding our microbial planet. Trends Microbiol. 24, 425–427 (2016). Article CAS PubMed Google Scholar Winkler, T. W. et al. Quality control and conduct of genome-wide association meta-analyses. Nat. Protoc. 9, 1192–1212 (2014). Article PubMed PubMed Central Google…
IJMS | Free Full-Text | Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761
1. Introduction The alarming decline of biodiversity worldwide necessitates urgent conservation measures, particularly for wild, endangered, and understudied species. According to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species, of the 5973 mammal species assessed, 1340 were classified as threatened with extinction, including 233 critically…
DETECTING GENETIC ENGINEERING WITH A KNOWLEDGE-RICH DNA SEQUENCE CLASSIFIER
Abstract Detecting evidence of genetic engineering in the wild is a problem of growing importance for biosecurity, provenance, and intellectual property rights. This thesis describes a computational system designed to detect engineering from DNA sequencing of biological samples and presents its performance on fully blinded test data. The pipeline builds…
Environment and taxonomy shape the genomic signature of prokaryotic extremophiles
Supervised machine learning analysis of the Temperature Dataset and the pH Dataset Supervised classification by taxonomy, environment category, and random label assignment Several supervised machine learning computational tests were performed to classify the Temperature Dataset and the pH Dataset, respectively, using (1) taxonomy labels (domain), (2) environment category labels, and…
Fast and robust metagenomic sequence comparison through sparse chaining with skani
Sequence identity estimation Formally, let G be a string of nucleotides and \({G}^{{\prime} }\) be a mutated version of G where every letter is independently changed to a different letter with probability θ. We will define the true ANI to be equal to 1 − θ under our model. Under the usual…
Whole genomes from bacteria collected at diagnostic units around the world 2020
Preparation of partners to collect samples Partners registered for participation by contributing isolates or DNA samples to the study. Material was sent to partners according to their registered participation format. This included material for sample collection, metadata registration, DNA extraction and sample shipment to Denmark. Specific protocols were provided, according…
Clustering-predicted structures at the scale of the known protein universe
Structural clustering algorithm The clustering procedure is similar to MMseqs2’s clustering but, instead of using sequences, Foldseek’s 3Di alphabet (Extended Data Fig. 1) was used to represent the structures as one-dimensional sequences. The clustering algorithm combines Linclust17 and cascaded MMseqs2 (ref. 42) clustering. The pipeline applies this strategy to allow for efficient…
The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data
Sample collection and DNA extraction An individual E. imbricata was obtained from the sea turtle rescue base on Naozhou Island, Zhanjiang City, Guangdong Province, China. A 10 mL blood sample was drawn from its jugular sinus and rapidly frozen for further analysis. Genomic DNA was extracted from the processed blood samples…
Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains
Identification and assembly of C. tetani-related genomes from aDNA samples To explore the evolution and diversity of C. tetani, we performed a large-scale search of the entire NCBI Sequence Read Archive (SRA; 10,432,849 datasets from 291,458 studies totaling ~18 petabytes; June 8, 2021) for datasets potentially containing C. tetani DNA…
Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. PNAS 113, 5970–5975. doi.org/10.1073/pnas.1521291113 (2016). Article ADS CAS PubMed PubMed Central Google Scholar Hahn, M. W., Koll, U. & Schmidt, J. The Structure and Function of Aquatic Microbial Communities (Springer International Publishing, 2019). Rosenberg, E., DeLong, E….
Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes
Strain identification The strain Phoma sp. CNCM I-4278 was previously isolated from the rhizosphere of Nicotiana tabacum (cv Xanthi, Solanaceae) grown under controlled conditions17. The fungus was identified according to the closest similarity of its 18 S rRNA sequence (HM16174323) with those present in GenBank by that time and it was…
SCELSE Seminar Series: A new binning method for genome recovery from long read metagenome data
Abstract:The recent development of long read DNA sequencing is poised to make a very substantial impact on the field of the microbiome science, particularly in relation to the problem of recovering metagenome–assembled genomes (MAG) from whole community metagenome data. I will outline a new genome binning method we have developed…
Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities
Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. New Phytol. 2015;206:1196–206. doi.org/10.1111/nph.13312. Article PubMed Google Scholar Zhou J, Ning D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiol Mol Biol Rev. 2017;81. doi.org/10.1128/MMBR.00002-17. Fitzpatrick CR, Salas-González…
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Publicly available mock community sequencing datasets 136 mock community sequencing samples were collected in total from four publicly available sequencing datasets and analyzed in our evaluation. 69 samples are from Lluch et al.33; 33 samples are from Kozich et al.34; 29 samples are from Fouhy et al.35; and 5 samples…
MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets
MArVD2 is a random forest classifier, implemented in the scikit-learn python package for novel archaeal virus discovery (Fig. 1) [61] where it’s trained and tested with separate datasets of archaeal viruses to best represent its performance in a variety of environments (Fig. 1). Integrating MArVD2 with machine learning introduces several practical and…
Dithiotreitol and Next Generation Sequencing of Bacterial 16S rRNA Shows Similar Diagnostic Security as Periprosthetic Tissue Cultures to Diagnose PJI
Introduction The need for a revision of a total joint replacement can be caused by various complications. The most common reasons for revision surgery are aseptic loosening, malpositioning of the implant and Periprosthetic Joint Infections (PJI) [1]. The incidence of PJI is lower than the incidence of aseptic loosening [2],…
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…
Metagenomes Assembles Genomes from cultivated freshwater bacterial communities
This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL)…
Building a mappability mask with SNPable
I am trying to build a mappability mask with Heng Li’s SNPable program lh3lh3.users.sourceforge.net/snpable.shtml . The instructions there are pretty brief and do not detail all the necessary steps, which makes it challenging for introductory bioinformaticians. Suppose the reference genome is genome.fa, copy-pasting the given instructions, they are: Extract all…
Extract the true single-cell RNA sequencing reads for running SAHMI
Hello everyone! I’m currently using the SAHMI pipeline to annotate microbiome information from the single-cell data. However, I encountered two potential problems when applying SAHMI to 10X scRNA data: The first one is that SAHMI (SAHMI)inputs both paired reads to annotate microbiome by using kraken2, which calculates k-mer of assigned…
Evolutionary genomics of camouflage innovation in the orchid mantis
Sample collection Captive breeding individuals of H. coronatus (Mantodea, Hymenopodidae) hatched from the same ootheca that was collected from the Xishuangbanna rainforest, Yunnan Province, China in 2018. Individuals of D. lobata (Mantodea, Deroplatyidae) were collected from a captive breeding center in Beijing, China in 2018. All individuals were housed in semitransparent…
Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China
Wu, Z. Antibiotic Use and Antibiotic Resistance in Food-Producing Animals in China OECD Food, Agriculture and Fisheries Paper No. 134 (OECD, 2019); doi.org/10.1787/4adba8c1-en Looft, T. et al. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl Acad. Sci. USA 109, 1691–1696 (2012). Article ADS CAS PubMed PubMed Central Google…
Foreign DNA detection in genome-edited potatoes by high-throughput sequencing
In addition to the k-mer method, several methods have been proposed to detect foreign genes in plants using NGS data. FED6 and CTREP-finder7 are mapping-based foreign DNA detection programs that require reference genome information. Recently, potato reference genomic sequences have been reported8,9; however, because of the variation in different cultivars,…
How to find the coverage of the assembled contigs of the PacBio long reads?
How to find the coverage of the assembled contigs of the PacBio long reads? 1 Hi, I have assembled the 3-cells reads data of PacBio HiFi. Question is how can I find the coverage of my assembled contigs? I shall be grateful to you. PacBio assembly coverage • 48 views…
Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism
Harley, R. M. et al. Labiatae. in Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants (ed. Kadereit, J. W.) vol. 7 167–275 (2004). Kokkini, S., Karousou, R. & Hanlidou, E. HERBS | Herbs of the Labiatae. Encyclopedia of Food Sciences and Nutrition 3082–3090 (2003) doi.org/10.1016/B0-12-227055-X/00593-9. Hao, D….
Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…
Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes
Sample collection, library construction and sequencing Leaves of two diploid C. paliurus (PG-dip and PA-dip) and one auto-tetraploid (PA-tetra) for genome sequencing were collected from plants grown in germplasm bank of C. paliurus, which located in Baima experimental field, Nanjing, Jiangsu province, China. After collecting, tissues were immediately frozen in…
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
Luo, Y. et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 48, D882–D889 (2020). Article CAS PubMed Google Scholar Korkmaz, G. et al. Functional genetic screens for enhancer elements in the human genome using CRISPR–Cas9. Nat. Biotechnol. 34, 192–198 (2016). Article CAS PubMed …
Bioinformatics Defines Semi-Extractable RNAs across Cell Lines
Researchers in Japan say they have developed a novel bioinformatic pipeline to define semi-extractable RNAs across human cell lines. Their findings “Landscape of semi-extractable RNAs across five human cell lines” appear in Nucleic Acids Research. The study provides new perspectives on exploring the involvement of RNA in biological processes such…
Indexing the human pangenome draft
Indexing the human pangenome draft 0 Hi, I am attempting to create a VG index against the human pangenome draft using vg autoindex. Here is the command: vg autoindex –gfa hprc-v1.0-mc-grch38-minaf.0.1.gfa –tmp-dir /home/ec2-user/pangenome/tmp vg has been running for about a week now and I’ve seen the following in the logs…
Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor
Crutzen, P. J. The influence of nitrogen oxides on the atmospheric ozone content. Q. J. R. Meteorol. Soc. 96, 320–325 (1970). Article Google Scholar Johnston, H. Reduction of stratospheric ozone by nitrogen oxide catalysts from supersonic transport exhaust. Science 173, 517–522 (1971). Article CAS PubMed Google Scholar Hughes, M. N….
First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]
Introduction Vultures are obligate scavengers, birds of prey that provide several ecological services such as nutrient recycling or avoiding soil contamination by carcass feeding, which help to reduce the spread of diseases in their habitats (Ogada, Keesing & Virani, 2012; Chung et al., 2015; Buechley & Şekercioğlu, 2016). Vultures are…
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…
Patterns and determinants of the global herbivorous mycobiome
Sampling overview A total of 661 samples belonging to 34 species and 9 families of foregut-fermenting ruminant (thereafter ruminant, n = 468), foregut-fermenting pseudoruminant (thereafter pseudoruminant, n = 17), and hindgut fermenters (n = 176) were examined (Fig. 1a, b, Supplementary Data 1). The dataset also provides a high level of replication for a variety of animals (229…
MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome-assembled genomes
Abstract We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is alignment-free, with k-mer frequencies being the only feature used to distinguish a DNA sequence from another (herein k = 7). MT-MAG is capable of classifying large…
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…
KaScape: A sequencing-based method for global characterization of protein-DNA binding affinity
Abstract It is difficult to exhaustively screen all possible DNA binding sequences for a given transcription factor (TF). Here, we develop a method named “KaScape”, by which, TFs bind to all possible DNA sequences in the same DNA pool where the DNA sequences are prepared by randomized oligo synthesis and…
The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes
Purohit, J., Kumar, A., Hynniewta, M. & Satyawada, R. R. Karyomorphological studies in guar (Cyamopsis tetragonoloba (Linn.) Taub.)—An important gum yielding plant of Rajasthan, India. Cytologia 76(2), 163–169 (2011). Article Google Scholar Gillett, J. B. Indigofera (Microcharis) in tropical Africa with the related genera Cyamopsis and Rhynchotropis. H.M.S.O Kew Bull.,…
OTU, ASV and Kraken2
OTU, ASV and Kraken2 0 Hello everyone, I’m seeking clarification on the relationship between OTU, ASV, and Kraken2, which confuses me. I understand that with the OTU approach, sequences are grouped into clusters if they have a similarity above a pre-set threshold, and these sequences are then compared to a…
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Grimont PAD, W. F. X. Antigenic formulae of the Salmonella serovars, 9th ed. (World health organization collaborating center for reference and research on Salmonella, Insitut Pasteur, 2007). Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ….
Transposons contribute to the acquisition of cell type-specific cis-elements in the brain
De novo motifs with high variability in chromatin accessibility across cells are similar to known binding motifs of neural differentiation-related transcription factors To discover accessible DNA motifs that are important for cell-type specificity in the mouse adult prefrontal cortex (P56), we first investigated whether cell types are characterized by k-mer…
A graph-based genome and pan-genome variation of the model plant Setaria
Variation and evolution in Setaria We collected genome-wide resequencing data for 630 wild (S. viridis), 829 landrace and 385 modern cultivated accessions from the Setaria genus with an average sequencing depth of ~15×, of which 1,004 were newly generated and 840 were from previous studies16,21 (Supplementary Table 1). After aligning…
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…
Biomedicines | Free Full-Text | High-Accuracy ncRNA Function Prediction via Deep Learning Using Global and Local Sequence Information
1. Introduction In recent years, growing access to massive transcriptome sequencing technologies has led to the discovery of an increasing number of novel transcripts from various species. The majority of these transcripts result in non-coding ribonucleic acid (ncRNA) molecules, short sequences of RNA that, with the exception of a small…
Characterization of metagenome-assembled genomes from the International Space Station | Microbiome
Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…
Illumina Complete Long Reads software analysis workflow for human WGS
Introduction Next-generation sequencing (NGS) enables scientists to decipher the genome for a deeper understanding of biology. Proven Illumina sequencing by synthesis (SBS) chemistry combined with award-winning DRAGEN secondary analysis delivers whole-genome sequencing (WGS) data with outstanding accuracy.1,2 DRAGEN Multigenome (graph) further improves mapping accuracy in challenging regions by ~50%.1 Still,…
The inchworm process failed. Trinity running error.
The inchworm process failed. Trinity running error. 0 Hello everyone, I’m trying to perform a de novo transcriptome using Trinity and having many issues. The last time I got the inchworm error attached. ******************************************************************** ** Warning, Trinity cannot determine which version of Java is being used. Version 1.7 is required….
Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales
Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…
Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
Adamek, M., Spohn, M., Stegmann, E. & Ziemert, N. Mining bacterial genomes for secondary metabolite gene clusters. Methods Mol. Biol. 1520, 23–47 (2017). CAS PubMed Google Scholar Belknap, K. C., Park, C. J., Barth, B. M. & Andam, C. P. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces…
CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization | BMC Bioinformatics
Datasets To verify the effectiveness of the CircSSNN, we adopted 37 circRNA datasets as benchmark datasets following the baselines we compared [15, 16]. We first downloaded the datasets from the circRNA interactome database (circinteractome.nia.nih.gov/). Subsequently, we obtained 335,976 positive samples and 335,976 negative samples following the process of iCircRBP-DHN [17]….
An unusual tandem kinase fusion protein confers leaf rust resistance in wheat
Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…
A preliminary study of the use of MinION sequencing to specifically detect Shiga toxin-producing Escherichia coli in culture swipes containing multiple serovars of this species
Tarr, P. I., Gordon, C. A. & Chandler, W. L. Shiga toxin-producing Escherichia coli and haemolytic uremic syndrome. Lancet 365, 1073–1086 (2006). Google Scholar Koudelka, G. B., Arnold, J. W. & Chkraborty, D. Evolution of STEC virulence: Insights from the antipredator activities of shiga toxing-producing E. coli. Int. J. Med….
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA-Protein Interaction Prediction
Noncoding RNAs (ncRNAs) play crucial roles in many cellular life activities by interacting with proteins. Identification of ncRNA-protein interactions (ncRPIs) is key to understanding the function of ncRNAs. Although a number of computational methods for predicting ncRPIs have been developed, the problem of predicting ncRPIs remains challenging. It has always…
Hybrids of RNA viruses and viroid-like elements replicate in fungi
Ribozyme search of the Sequence Read Archive Observing that ribozymes are sufficiently short to be captured on a short sequence read (less than 100 nt), we reasoned it will be possible to screen large volumes of sequencing data to identify libraries potentially containing ribozyme agents. To this end we adapted…
A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)
Ethics statement All animal experimental procedures were approved by the Biomedical Ethics Committee of Qufu Normal University (approval number: 2022001). Sampling and sequening The experimental sample is a wounded male duck found during the wild bird survey in Jiangsu, China, which died unexpectedly during rescue. We dissected the sample and…
error in Genome Mepping by BWA tools in Linux
$ gmap_build -D:\btau8refflat.gtf Unknown option: D:btau8refflat.gtf -k flag not specified, so building main hash table with default 15-mers -j flag not specified, so building regional hash tables with default 6-mers gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP. Part of GMAP package, version…
Introducing GPMeta: Ultrarapid GPU-accelerate | EurekAlert!
image: Runtime of GPMeta versus existing solutions view more Credit: BGI Genomics Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in the dry-lab step of mNGS tests. However, this…
Phenotypic and Genetic Analysis of KPC-49
Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…
kallisto bootstrap / condo installation problem
kallisto bootstrap / condo installation problem 0 I have used kallisto in the past, but am now struggling to get it to work on a new computer (MacBook M1). When I download kallisto using brew, and try to run kallisto quant, I get an error not generating bootstraps ‘Warning: kallisto…
An apicomplexan parasite drives the collapse of the bay scallop population in New York
Lafferty, K. D., Porter, J. W. & Ford, S. E. Are diseases increasing in the ocean?. Ann. Rev. Ecol. Evol. Syst. 35, 31–54 (2004). Article Google Scholar Ward, J. R. & Lafferty, K. D. The elusive baseline of marine disease: Are diseases in ocean ecosystems increasing?. PLoS Biol. 2, 542–547…
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
State-of-the-art phylogenomic pipelines require many steps, which can be both time consuming and error prone (Fig. 1a). With Read2Tree, we directly process raw sequencing reads and reconstruct sequence alignments for conventional tree inference methods (Fig. 1b and Supplementary Fig. 1). We start by aligning raw reads to nucleotide sequences derived…
Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia
Burger, G., Gray, M. W. & Lang, B. F. Mitochondrial genomes: Anything goes. Trends Genet. 19, 709–716 (2003). Article CAS PubMed Google Scholar Hawksworth, D. L. & Lücking, R. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spectr. 5, 5–4 (2017). Article Google Scholar Theelen, B., Christinaki, A. C.,…
NGS: Sequence QC – Texas A&M HPRC
Back to Bioinformatics Main Menu Evaluation FastQC GCATemplates available: grace terra module spider FastQC After running FastQC via the command line, you can ssh to an HPRC cluster enabling X11 forwarding by using the -X option and view the images using the eog tool. From your desktop: ssh -X username@grace.hprc.tamu.edu From your FastQC working…
removing lines of code from a function?
I’m working on a project for a bioinformatics class. We are given various DNA strings and an integer k for the project. The project’s goal is to identify a K-mer motif that minimises the total of the hamming distances between the motif and each DNA strand. So, first, look at…
Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling | Genome Biology
Benchmark setup We first developed a basecalling benchmarking framework enabling new and existing basecalling algorithms to be easily compared. Moreover, our benchmark facilitates the study of individual components of basecallers, as different combinations of basecaller components can readily be evaluated. The framework is divided into two main components: (i) standardized…
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS PubMed PubMed Central Google Scholar Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS PubMed Google Scholar Peralta, I. E., Spooner, D. M. & Knapp, S….
The Biostar Herald for Monday, April 03, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
poor classification using qiime2 – User Support
Good morning, I am experiencing some difficultie sto get results even if indeed my pipeline has not changed.In specific what I obtain is kind of poor classification: half of the sequences (very low number of OTU in addition (e.g 900) are just attributed to Bacteria or OD1. So I think…
Chromosome-level genome assembly of the critically endangered Baer’s pochard (Aythya baeri)
Ethics statement All animal handling and experimental procedures were approved by the Qufu Normal University Biomedical Ethics Committee (approval number: 2022001). Sample and sequencing Baer’s pochard tissue for whole-genome sequencing was obtained from a dead individual that had strayed into a fishing net in Shandong (China). The muscle tissue that…
Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition
. 2023 Mar 22;18(3):e0282428. doi: 10.1371/journal.pone.0282428. eCollection 2023. Sarah K Highlander 1 , Jason M Wood 2 , John D Gillece 1 3 , Megan Folkerts 1 , Viacheslav Fofanov 3 4 , Tara Furstenau 3 , Nitin K Singh 2 , Lisa Guan 2 , Arman Seuylemezian 2 , James N Benardini 2 , David M Engelthaler …
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article Google Scholar Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…
Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome
Introduction Cyanide-containing compounds are known as nitriles and are widely distributed in the natural environment. They are generated by different plants in various forms, such as ricinine, phenyl acetonitrile, cyanogenic glycosides, and β -cyanoalanine (Sewell et al., 2003). Anthropogenic activities have substantially influenced the production of vast quantities of nitrile…