Tag: ROH

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

Goldberg JL, Klassen MP, Hua Y, Barres BA. Amacrine-signaled loss of intrinsic axon growth ability by retinal ganglion cells. Science. 2002;296:1860–4. Article  CAS  PubMed  Google Scholar  Blackmore M, Letourneau PC. Changes within maturing neurons limit axonal regeneration in the developing spinal cord. J Neurobiol. 2006;66:348–60. Article  CAS  PubMed  Google Scholar …

doi: 10.1007/978-1-0716-3084-6_12. Affiliations Expand Affiliation 1 Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. tyroh@postech.edu. Item in Clipboard Tae-Young Roh. Methods Mol Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1007/978-1-0716-3084-6_12. Affiliation 1 Department of Life Sciences, Pohang University of Science…

Entry EC 1.4.3.19                 Enzyme                                  Name Class Oxidoreductases;Acting on the CH-NH2 group of donors;With oxygen as acceptorBRITE hierarchy Sysname glycine:oxygen oxidoreductase (deaminating) Reaction(IUBMB) glycine + H2O + O2 = glyoxylate + NH3 + H2O2 (overall reaction) [RN:R00366]; (1a) glycine + O2 = 2-iminoacetate + H2O2 [RN:R07463]; (1b) 2-iminoacetate + H2O = glyoxylate +…

Environmental factors are one of the forces influencing agricultural and the livestock sectors. Animals exposed to stressful environments exhibit various adaptive mechanisms, such as behavioural, physiological, endocrine, cellular, metabolic and biochemical for minimising the stressful conditions. Thus, adaptation is the natural strategy to ensure both welfare and efficiency. The action…

Sample collection We obtained the short read sequences for 33 brown bear genomes, four polar bears (Ursus maritimus) and two American black bears (Ursus americanus), publicly available from NCBI’s SRA repository (Table S1 and Fig. 1a)12,13,15,16,40,51,65. Next, we selected from our private collections a total of 95 additional samples for sequencing, among…

In the absence of a standardized definition of ocular myasthenia gravis (OMG) from established diagnostic criteria, researchers of a new retrospective, single-center study say that OMG should be considered in patients with both ptosis and diplopia, particularly vertical diplopia. Further, they suggest that high acetylcholine receptor auto-antibody (AchR Ab) titer,…

Filtering methods for samtools or GATK 1 Hello everyone! I just started my PhD and my level of expertise is fairly low about bioinformatics! Is there any advice regarding different covarege levels?( 10x vs 50x or more ). I would need simple instructions for filtering using either samtools or GATK….

Tuttle KR, Bakris GL, Bilous RW, Chiang JL, de Boer IH, Goldstein-Fuchs J, et al. Diabetic kidney disease: a report from an ADA Consensus Conference. Diabetes Care. 2014;37(10):2864–83. Article  Google Scholar  Jha V, Garcia-Garcia G, Iseki K, Li Z, Naicker S, Plattner B, et al. Chronic kidney disease: global dimension…

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

Horses have been considered one of our most prized possessions, used for travel, work, food, and pleasure for at least five and a half millennia17,18,19,20. Nevertheless, the ancestry of various horse breeds and their characteristic traits remains unclear21. In this paper, we describe the patterns and the origins of genetic…

What is SNP array testing? The SNP array test looks for changes in specific areas of a person’s chromosomes, such as gains (duplications) or losses (deletions). These gains or losses result in extra or missing copies of genetic material. How does SNP array work? SNP array is a type of…

plotting roh from bcftools 0 Heys, I am following this small tutorial on how to calculate ROHs from a vcf file using bcftools (samtools.github.io/bcftools/howtos/roh-calling.html) and I am getting this txt file: # This file was produced by: bcftools roh(1.10.2+htslib-1.10.2-3) # The command line was: bcftools roh -G30 –AF-dflt 0.4 my_file.vcf…

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

Interpreting output of BCFtools RoH 0 Hello! I am using BCFtools RoH for the first time, and I am having some trouble understanding its output file. The input is a gvcf file with genotype calls for one sample only, and I want to infer where there might be autozygous tracts….