How can I find UTR region sequence of a particular bacteria mRNA with the help of bioinformatics?

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Marker gene metagenome sequencing?

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fluorescent imaging without fixatives?

How to store SDS-PAGE for fluorescent imaging without fixatives? I am running protein samples on SDS-PAGE that are tagged with fluorophores. If I place the gel in a destain solution of...

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Is a 5` phosphate needed for homologous recombination?

Is a 5` phosphate needed for homologous recombination? I am a bit confused whether phosphorylated DNA is needed to achieve efficient homologous recombination in e coli. I believe there are methods...

06 June 2024 7,065 1 View

Diluting an enzyme before an experiment?

What is the reason or importance of diluting an enzyme before an experiment? I'm writing a report on enzyme activity and characterisation and i need help with understanding this: we were told to...

06 June 2024 8,714 2 View

How do you get Rid of Nonspecific Bands in PCR?

So, here is what I am dealing with: The Tm of the primers is 55 for the forward one and 56 for the reverse one. In -silico PCR produces 750 BP band, but in reality I get 3 bands. The third one...

17 March 2024 9,914 5 View

PCR nonspecific product?

I am amplifying target sequence 450 bp. I get single sharp band in the control and faint in sample with another sharp nonspecific product. why? I need to get one single band from my sample to...

17 March 2024 804 3 View

CRISPR targeting in cell line, flow or single clone?

I am doing a CRISPR targeting to knock out one intron of my gene of interest in a cancer cell line and replace that intron with GFP. I am wondering if I should pick single cell clone with possible...

17 March 2024 9,713 1 View

How convert Bacterial DNA concentration to copy numbers?

For example, If a PCR primer can detect ~100 fg of DNA, how we will calculate it to Bacterial copy number?

17 March 2024 1,816 2 View

Guide RNA for improved CRISPR-Cas9 gene editing ?

How can the design and synthesis of guide RNA molecules be optimized for improved CRISPR-Cas9 gene editing?

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Can it be used for large gene production (4 kbp) via CRISPR-mediated HDR?

I could not find a study that used CRISPR-mediated HDR for stable integration of large genes. I would be grateful if anyone could point me in the right direction.

05 August 2023 486 2 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

The Optimal Experimental Approach for Gene Function Analysis?

What is the most suitable experimental setting to understand the consequences of a particular gene: (1) targeted degradation of the specific transcription factor (TF) of the gene, followed by...

04 August 2024 6,264 1 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

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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

Optimal siRNA Volume for Complexation with Liposomes in a 2.5 mL Solution with 10 mg/mL Lipid Concentration?

How much volume of siRNA can I add to 2.5 mL of liposomes with a total lipid concentration of 10 mg/mL?

27 July 2024 6,920 1 View

How to transfect circular mRNA to T cells?

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What happens in snapTotal- seq?

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Printing residues in an object in Pymol?

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15 July 2024 1,727 1 View

Can I detect the FLAG sequence of my AAV vector by qPCR?

I am treating human cells with an AAV vector encoding for my gene of interest tagged by FLAG. I want to quantify the mRNA expression of my gene of interest via qPCR to discriminate the endogenous...

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Hari Shankar Gadri

Hii

Moein

several tools are available for gene prediction, it is determined UTR region.

Niloofar Khakpour

Hi,

UTRscan server

Ankur Das

Blast search the full ORF with the genome, you can then manually mine the promoter region, later check for the presence of regulatory elements associated with the gene function for validation