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 7,707 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 6,553 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 8,643 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 1,174 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 2,830 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 625 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 294 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 582 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 4,144 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 9,771 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

Is there any way to quantify bacterial and fungal cells in their mixed culture?

I am working in fungal fermentation of soybean meal and there is bacterial growth in them at times. I am trying to quantify fungal cell counts and bacterial cells; but I haven't been able to do at...

07 August 2024 7,535 4 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View