What is the best "in silico PCR" sites for bacteria that can be used?

More Moein Iranmanesh's questions See All

Marker gene metagenome sequencing?

The source of classification bias in marker gene metagenome sequencing? a variability in the taxonomy classification of microbial communities when using different primer pairs (e.g. for 16S rDNA)...

29 June 2024 1,048 1 View

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...

29 June 2024 8,720 1 View

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?

05 August 2023 1,375 2 View

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

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 5,137 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 1,667 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 4,731 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

What precautions should be taken while handling S. aureus enterotoxin Type B in the lab?

I would like to understand potential safety concerns while handling SEB in the lab. Especially while working in animal house facility. Would like to know precautions for handling. Sigma MSDS...

07 August 2024 6,032 3 View

How to understand this crystallographic phenomenon of low temperature crystals in zeolite?

During low-temperature testing, new diffraction peaks that appear could be indicative of several phenomena. In one of our tests, we observed notable new peaks around 40° and 45° in a specific...

06 August 2024 725 3 View

How much total RNA concentration to be extracted from sorted plasma cells from bone marrow of C57BL/6 mice for RT-PCR ?

i have sorted anti-NP specific plasma cells from bone marrow of C57BL/6 mice at certain times after immunization with variable counts and isolated total RNA using TRIZOL method for RT-PCR using...

05 August 2024 8,835 1 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 9,056 3 View

"A Markov-like Model for Patient Progression"?

A Markov-like Model for Patient Progression" Markov Chain Monte Carlo (MCMC) Markov Chain Monte Carlo (MCMC) is a powerful computational technique used to draw samples from a probability...

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Fatemeh Yaghoobiadeh

Hello

The following servers may be usefull. You can try them.

1 UCSC Genome Browser

https://genome.ucsc.edu › hgPcr

UCSC In-Silico PCR

2. In-silico.com

3 UPV/EHU

http://insilico.ehu.es › PCR

In silico PCR amplification

Claudia Angélica García Alonso

Hello! I'd recommend trying Benchling for PCR and other molecular biology in silico assays

Cloud-based platform for biotech R&D | Benchling