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Questions related to Bioinformatics
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 8,044 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 1,266 3 View
Kit used: MN - Nucleospin Gel and PCR cleanup kit
21 December 2022 3,608 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 4,139 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 4,778 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 8,020 4 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 223 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 3,704 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 5,930 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 8,507 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 7,802 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 6,084 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 838 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 1,269 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 1,410 0 View
I have to add protease inhibitor and phosphatase inhibitor during cell lysis in a six well plate. How can i calculate the amount of protease and phosphatase inhibitor amount ?
08 March 2022 259 1 View
Hello, I am struggling to interpret couple of splice site mutations I have encountered and I would like to ask if there is a way to predict the outcome of a given splice site mutation (does it...
02 March 2022 7,914 1 View
I have the problem, like several other people before, that large proteins get lost during electrophoresis in the SDS PAGE gel. All protein bands below 80 kDa are perfectly separated as usual, the...
18 October 2021 5,987 8 View
I want to identify gene duplication events of specific genes between particular plant species. I also want to calculate the Ka and Ks value between the duplicated genes. It would be a great help...
03 October 2021 6,873 3 View
Currently I have the code to compare the ED50 values among different treatments = compParm(res2, strVal="e"). What would the code be for a different ED value?
29 July 2021 9,670 1 View
Dear experts, I am trying to set up my annealing protocol to make dsDNA out of 2 ssDNA oligos (29 nucleotides each). I have both oligos in the same 100 uM concentrations and use 40 ul of each....
07 July 2021 5,637 1 View
I have installed the tool Raccoon in ubuntu. I was able to open it and load ligands, receptors , grid and dpf files successfully. However, I could not able the run the command ./RunVS.sh as it...
27 June 2021 711 0 View
For PTM site prediction through In Silico method, I try to use this server but it is not responding. Please help me to solve the problem. Thanks in advance.
23 May 2021 2,782 4 View
In western blot, primary antibody usually incubates overnight at 4°C. But the signal after incubation for 1-2 hours at room temperature is also strong enough to detect. If I incubate at room...
13 May 2021 1,652 3 View