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Tag: MUMmer
Seroprevalence and Molecular Characterization of B. abortus
Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…
A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes
Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article CAS PubMed Google Scholar International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….
Annotate Unplaced Scaffold with Chromosome Information
Annotate Unplaced Scaffold with Chromosome Information 0 I have a genome that has been assembled to a scaffold level, and a chromosome level genome from a related species. My desire is to annotate the scaffolds with chromosome information from the chromosome level assembly. My current plans are to do so…
Alignment with Big Target (Reference) File
Alignment with Big Target (Reference) File 0 Hello! I have a 900 GB eukaryotic nucleotide sequence Fasta file that I downloaded from NCBI. I want to align my query sequence (for now only one for testing purposes). For that I tried LASTZ, Nucmer, and blast. Since I have a extremely…
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 …
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…
Bioinformatics Scientist – Noralogic Inc
Job Title: Bioinformatics Scientist Job Location: Bethesda , MD (20892) Job Type: Contract (Onsite) General Summary Additional Qualifications – Master’s degree in Bioinformatics or a related discipline – Two years’ experience Field of Study Biochemical Sciences Information Sciences Software MS Office R PowerPoint Unix Image J Outlook Python JAVA C++…
How to create structural variants ground truth for alignment of two long-read genome assemblies?
Hello everyone, I’m a student in the area of genomics. I have two genome assemblies from long reads (from haploid genomes). One is the reference of the organism (K. phaffii, a yeast), which represents the wild type. The other (the query) is an assembly of an K. phaffii strain, which…
Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia | Parasites & Vectors
The following results clearly demonstrate that the Borrelia spp. identified in ticks collected from V. salvator, V. varius, and V. giganteus are distinct species. Therefore, for clarity, we herein refer to these Borrelia spp. by their proposed names: Borrelia salvatorii (from V. salvator), ‘Ca. Borrelia undatumii’ (from V. varius), and…
26 All paired end Illumina libraries were inspected with FastQC v0115
26All paired-end Illumina libraries were inspected with FastQC v0.11.5() and trimmed and filteredwith Trimmomatic v0.36 (66). Read mapping was performed with sppIDer pipeline(81) using a combined reference including the genome assembly of CBS9595 (asrepresentative of P1 lineage, Supplementary File 1 for more details) and CBS14141(as representative of P2 lineage, Supplementary…
Very few snp and indels variation were identified using PAV variation input file base on vg call
Very few snp and indels variation were identified using PAV variation input file base on vg call 0 Hi all, We want to find the snp and indels variation from the result vcf file BS_graph_call.vcf by using the pan_genome vg analysis software. There are only **fewer than 20 snp and…
Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants
1. Introduction Tuberculosis (TB) is a significant global burden and is widely reported to be a major public health and economic problem, costing the world $617 billion between 2000 and 2015 and projected to cost $1 trillion between 2015 and 2030 (1). It is the second leading cause of death…
Identifying Mutation Frequency Changes in MSAs over time?
Identifying Mutation Frequency Changes in MSAs over time? 0 Hello, I have 6 sample fasta files total over 3 time points: WEEK 3, 5 & 7. There are two samples per time-point which are Control and Positive for a Specific Gene. These samples are YU2 HIV viral transcriptomes. In each…
Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags
1. Introduction Melioidosis is a tropical disease caused by the aerobic, Gram-negative motile bacillus which is classified as a category B biological agent by the Centers for Disease Control and Prevention (CDC) of America (1, 2). It is a highly pathogenic endemic zoonotic disease in many tropical countries, particularly in…
Whole genome comparison of two closely related plant species
Whole genome comparison of two closely related plant species 0 Dear all, I want to compare two closely related plant species, (Arabidopsis thaliana, Brasica napa) and I am looking for the latest or the state of art tools to do that. What I want to find is regions that are…
mapping or denovo assembly of genome with big diversity (Chlamydomonas)?
mapping or denovo assembly of genome with big diversity (Chlamydomonas)? 0 I have question, as this is usually not my field of working at all! I’m used to work with bacterial genomes, but I have small project including Chlamydomonas mutants then I would like to ask experts what they are…
Has anyone here used the MAC tool for merging assemblies?
Has anyone here used the MAC tool for merging assemblies? 0 I’m relatively new to whole genome work and have been exploring various tools for assembling/mapping genomes. I’ve read that not all assembly tools/programs are created equal and often times it is valuable to assess assemblies from multiple tools for…
How to get the sequence differences between multiple bacterial genomes
How to get the sequence differences between multiple bacterial genomes 1 I am working on some closely related bacterial species (complete genomes from NCBI). I would like to extract the sequence differences between them. To be more specific, I want to find unique sequences (50 -100 nts) in each of…
Is it possible to do mummerplot with reference and query sequences that have many contigs?
Is it possible to do mummerplot with reference and query sequences that have many contigs? 0 Hi, I have a reference genome that has 9 contigs and query genome that has 56 contigs. They both has more than 99 % identical nucleotides. I tried to make mummerplot but got really…
Mapping transcripts to mitogenome
Mapping transcripts to mitogenome 0 I have performed de novo assembly of a plant mitogenome (non-model plant). In addition, I also perform de novo transcriptome assembly of this particular plant species. How to verify if the mitogenome assembly is correct making use of the RNA-Seq data? Should I align my…