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Questions related to Bioinformatics
I know that in LighterCycler 480 system, we can use Absolute quantification/fixed points methods and then set a reasonable noise band to estimate the CT values. My workmate told me to use this...
02 February 2023 2,578 3 View
I am working on immobilization of peroxidase on magnetic nanoparticles using adsorption. Unfortunately, the change in enzyme activity is very low. Consider the absorbance change over 3 mins for...
02 February 2023 1,149 3 View
Using AlphaFold, I have predicted protein structure models and lDDT plot. Is there a way to color each model based on lDDT values using PyMOL? Thank you in advance.
27 January 2023 8,768 4 View
Hello, collegues, I'm trying to estimate the distribution of a certain kind of microorganism (eg Methanobacterium) in a certain environment (permafrost) from metagenomic data presented on various...
19 January 2023 3,574 2 View
I'd like to sequence the genome of the gopher tortoise. The genomes of congeners are ~2.4Gb. I'm trying to decide how much coverage is necessary; we plan to run the sample on a portion of a...
13 January 2023 705 4 View
I am looking for a buffer solution to preserve the DNA in dissociated muscle cells at room temperature (because I need to transport them at room temperature). The cells do not have to be viable, I...
11 January 2023 5,285 2 View
Hello, I have band of my negative control. I am sure there is no contamination. I used new everything, sterile and change my gloves 5 times. I did negative control mix separately my samples. My...
03 January 2023 6,787 10 View
I am working on immobilization of peroxidase on magnetic nanoparticles, I want to study the influence of immobilization on pH, Temperature and kinetics of the enzyme. How to do so given that the...
02 January 2023 8,148 4 View
Can someone please list the analysis that needs to be performed to understand and compare the mechanism of a protein in its native and inhibitor-bound state? (NOTE: Not the interaction between...
25 December 2022 1,388 3 View
Kit used: MN - Nucleospin Gel and PCR cleanup kit
21 December 2022 3,716 3 View
Why is phenol-chloroform used in nucleic acid extraction and not any other solvent ? There are many solvents, but why only phenol-chloroform is used...
05 December 2022 4,263 2 View
Hi, I am using the same DNA template to run two 7kb PCR experiments with the same cycling conditions simultaneously. The only difference between the two experiments is the primer pair. One result...
03 December 2022 4,886 7 View
Hello, I am currently docking my ligand with a target and getting a positive binding energy in AutoDock while Vina gave expected negative value. What can be wrong with docking in AutoDock? Thank...
01 December 2022 8,099 4 View
Hey, I'm trying to optimize a molecule by using GAMESS US with solvent (water, PCM) while constraining Cs symmetry. When I add solvent the symmetry changes (C1) even though the GAMESS acknowledges...
22 November 2022 3,701 1 View
Hello, I have tried loading pro as the first amino acid on to the 2-chlorotrityl chloride resin (CTC) with no luck. I have performed both using manually synthesis and tried using the synthesizer...
17 November 2022 1,605 0 View
Hi, I'm looking for a product recommendation. I want to seal microplates containing bacteria for an overnight growth curve at 30-37 degrees C. The job of the seal is to keep moisture from escaping...
06 November 2022 354 3 View
Hello everyone I had a kinase+ATP-Mg complex. I ran MS simulation for 100 ns. via GROMACS and CHARMM36. The system is stable (backbone RMSD is and reach plateau before 20 ns.). When I used...
03 November 2022 3,818 11 View
I'm working with swabs collected from fish mucus to look for microbes but I am not sure about the right bead beating time and the number of cycles. Thank you!
21 September 2022 6,036 1 View
Does anyone know if Illumina adapter sequences have changed for NovaSeq 6000? I tried using the sequences described for HiSeq 2500 / TruSeq for trimming my raw data and it didn't work well for...
05 September 2022 8,616 7 View
Hi all, I want to download some reference microbiome data from NCBI sequence Read Archive (SRA). I previously used fasterq-dump or fastq-dump to download the data, and the data were used to be...
08 August 2022 7,882 1 View
Hi everyone, Here are the nanodrop reading values for DNA concentration after the chromatin de-crosslinking step followed by elution with 20 uL elution buffer. Sample ng/uL ...
23 June 2022 6,222 0 View
Hi everyone, I have the reagents to culture A549 Cells but don't know what volumes to use. I have DMEM, FBS, Pen/Strep, Amphotericin B. for growth. Could anyone advise me on volumes...
23 May 2022 959 1 View
Hi, I'm running an immunoprecipitation experiment, trying to pulldown actin from some RAW 264.7 cell homogenates. I ran a Western blot with a 1:5000 dilution of biotinylated anti-actin...
03 May 2022 1,434 0 View
I was wondering on the preparation of lyticase (sigma L2524-10KU). I could not find specifically on to prepare the stock solution to use in pulse field gel electrophoresis. Does any one know...
08 April 2022 1,508 0 View