Categories
Tag: GC-content
What are the factors that influence the bias of 16S rRNA gene ampicon sequencing?
What are the factors that contribute to coverage bias in amplicon sequencing?4 answersCoverage bias in amplicon sequencing can be influenced by several factors. These include differences in 3′-end stability, primer Tm, amplicon length, amplicon GC content, and GC content of amplicon flanking regions. The presence of a highly dominant taxon…
Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants
Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…
Comparison of methylation estimates obtained via MinION nanopore sequencing and sanger bisulfite sequencing in the TRPA1 promoter region | BMC Medical Genomics
Repeated measurements in one DNA sample revealed congruent results for methylation calling between the methods Sanger bisulfite and nanopore sequencing Mean methylation rates and the methylation rates of individual replicates were congruent between bisulfite and nanopore sequencing (Fig. 1), although the number of calls per site varied in nanopore sequencing. The…
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…
Next-Generation Sequencing (NGS): Revolutionizing Genomic Analysis
Next-generation sequencing is a revolutionary genomics technique that has transformed how we study and understand genetic information. It allows researchers to decode DNA at an unprecedented speed and scale, paving the way for groundbreaking discoveries. In the ever-evolving field of genomics, staying updated is not just an option; it’s a…
Learning the rules of the Scrabble game behind lymphocyte diversity
Reporter, terrier, retire, retro, port, trio, toe. What do these seemingly random words have in common? They can all be formed from bits and pieces of the word repertoire (hats off to any Scrabble fans in the audience). This concept—of adding, deleting, and rearranging the letters of a fixed character…
Unraveling variant misclassification: Insights from ClinVar and HGMD databases
Cardiac Comprehensive Kit analyzes 292 genes and covers major inherited cardiovascular disorders. Genes Tested AARS2, ABCA1, ABCC6, ABCC9, ABCG5, ABCG8, ACAD9, ACADVL, ACTA1, ACTA2, ACTC1, ACTN2, ACVR1, ACVR2B, ACVRL1, ADAMTS2, AFF4, AGK, AKAP9, AKT3, ALDH18A1, ALMS1, ALPK3, ANK2, ANKRD1, APOA5, APOB, APOE, ATP6V0A2, ATP6V1A, ATP6V1E1, B3GALT6, B4GALT7, BAG3, BGN,…
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotypic organization
↵* Corresponding author; email: skuraku{at}nig.ac.jp Abstract Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here,…
“Very close % of target vs % of Background sequences with Motif” & “SeqBias at 1st rank”
Homer motif analysis: “Very close % of target vs % of Background sequences with Motif” & “SeqBias at 1st rank” 1 Hi everyone. I’m trying to find the motifs bound by my ChIP-ed protein using Homer. I don’t have knowledge regarding NGS analysis. The analysis was done by my labmate…
what is gene synthesis used for
As the resulting plasmid contains the original prefix and suffix sequences, it can be used to join with more BioBricks parts. The development of the Golden Gate assembly methods and its variants has allowed researchers to design tool-kits to speed up the synthetic biology workflow. By using the BsaI restriction…
HOMER Results – SeqBias interpretation and follow-up
Hi everyone, I am using findMotifs from Homer to find enriched motifs in a set of genes of interest. This is the first time I am doing this and I’m a bit confused with some of the results. I am getting a lot of entries with SeqBias, with combinations of…
GC content of WES cohort
GC content of WES cohort 0 Hello, I know a lot of questions have been asked before about GC content, but I just wanted to see if anyone had experience with WES GC content. I have 134 WES (not all the same exome panel or from the same sequencing company)….
Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol | PLOS ONE – Molecular Biology Protocol – Restriction Digest of Plasmid …
Abstract A waxing variety of “genotype-by-sequencing” (GBS) methods use restriction enzymes and high throughput DNA ordering to generation data for a set of genomic loci, allowing the simultaneous discovery press genotyping of thousands of polymorphisms in a set of multiplexed samples. We evaluated a “double-digest” restriction-site associated DNA sequencing (ddRAD-seq)…
Gut taste receptor type 1 member 3 is an intrinsic regulator of Western diet-induced intestinal inflammation | BMC Medicine
Study design The objective of the study was to evaluate the influence of long-term WD intake on intestinal inflammation and investigate possible mechanisms by which WD intake could affect IBD development. To this end, mice were fed normal diet (ND) or WD for 10 weeks, and bowel inflammation was evaluated through…
GATK g CNV code Aborts Before Running Main Code
GATK g CNV code Aborts Before Running Main Code – Bioinformatics Stack Exchange …
rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses | BMC Bioinformatics
Case study To illustrate and evaluate the functionality of rprimer, two assays targeted at norovirus GI were designed. Assay A: RT-qPCR for quantitative detection of norovirus GI The first task was to design a broadly reactive RT-qPCR assay for quantitative detection. For this, we decided to use the ‘ambiguous’ primer…
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…
PacBio sequencing output increased through uniform and directional fivefold concatenation
Strategy and design of the method We sought to develop a simple method to increase the sequencing capability of PacBio CCS to sequence several diverse DNA libraries ~ 870 bp in length that encoded protein variants originating from a directed evolution campaign. To achieve an increase in the throughput of a PacBio sequencing…
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ?
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ? 0 A colleague of mine have got the following distribution of GC-content for RNAseq. How to interpret bimodal distribution of GC-content for RNAseq ? Does it mean some contamination ? Is there any method to…