Tag: GC-content

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…

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…

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 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…

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…

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,…

↵* 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,…

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…

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…

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 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)….

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)…

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 – Bioinformatics Stack Exchange …

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…

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…

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 ? 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…