What NGS platform should I pick for a genome with 6K size?

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Is it possible to use OD for comparing sample and control instead of positive of negative results?

If someone uses a cut-off ELISA kit, is it possible to use the ODs for comparison of sample data to control groups and not only report positive and negative?

09 October 2018 7,588 4 View

What happens if a system be not neutral in Molecular Dynamic Simulation?

Hi, Recently, I performed a MDS with Gromacs and did not neutralized the system. MD was ran and nothing happened. I wonder what will happen in a non-neutral MDS. Can it be used for analysis? Regards

08 September 2018 6,455 4 View

How to import and merge different pdb contents into one?

Hi there, I need to import a DNA molecule into a crystallographic pdb file containing a viral capsid. Furthermore, I want to add some ion molecule surrounding the viral structure. Is there any...

07 August 2018 8,524 5 View

What should be considered for imaging phage particles by TEM microscopy?

Hi there, I have a stock solution of a clinical isolated phage with a titre of ~3E12 pfu/ml. Is it high enough for TEM microscopy, and is there any other considerations for imaging? Regards Alireza

05 June 2018 1,089 2 View

Why extended simulation dose not start at 0 point?

Hi, I have extended my MDS using Gromax according to this: gmx convert-tpr -s md_1.tpr -extend 9400 -o md_2.tpr gmx mdrun -s md_2.tpr -cpi md_1.cpt -nb gpu -v However after simulation done, I...

04 May 2018 2,736 5 View

Do I have to remove outlires or keep them for analysis?

Hi there, I have a forest plot of a meta-analysis. From 13 studies with same method and same subjects I have 2 studies in same country, which are outliers. The studies have two different sample...

03 April 2018 531 9 View

How is it possible to evaluate fluctuations, flexibility, and stability of a certain domain within a protein after MDS with Gromacs?

Hi there, I want to know how can i determine fluctuations, flexibility, and stability of a certain stretches of amino acids (for example amino acids 20 to 50) within a protein after MDS with...

02 March 2018 211 1 View

After extending simulation, how can I make trajectories with full first-to-end simulation time?

Hi, I have extended a simulation from 10ns to 100ns with following command: gmx convert-tpr -s md_10ns.tpr -extend 90000 -o md_100ns.tpr and: gmx mdrun -s md_100ns.tpr -cpi md_10ns.cpt -nb gpu...

02 March 2018 480 1 View

Is it possible to use Paraffin-fixed biopsy sample for viral copy number quantification?

Hi there, I have found a paper presenting results in which human cytomegalovirus load has been assessed in biopsy samples. The paper did not mentioned whether the samples were paraffin-fixed or...

01 February 2018 4,052 3 View

How to clear the nanoparticle's dye after DNA extraction?

Hi, I have used a magnetic-based DNA extraction kit. At the final step, when I want to dissolve DNA from magnets in elution buffer (Triss-EDTA pH=8.5), the magnet dyes are dispersed into the...

31 December 2017 9,686 4 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Samples to study circular dichroism (chirality)?

I want to build a low-cost polarimeter to study circular dichroism (chirality). What type of samples can I use? I am looking for samples that can be found outside the laboratory.

01 March 2021 9,101 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

How do you mesh a thin solid in Fluent?

Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...

24 February 2021 8,856 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View