Query regarding Whole Genome Sequencing

More Saleha Masood's questions See All

How to solve g_mmpbsa error?

Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out

07 August 2024 6,066 0 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View

65% saturation of ammonium sulfate in 100 ml? (for protein precipitation)?

Hi All: I need to precipitate extracellular protein from supernatant. A bit confused with ammonium sulfate calculation. Should I be adding: 1. 65g of ammonium sulfate in 100 ml of...

09 July 2024 5,508 0 View

How to find the expected Kd value of a recombinant antibody?

We produced scFv of an antibody from bacteria. Now we want to establish dissociation Kd of antibody using quantitative elisa. How can i know the expected Kd value (range in nM, or mM)?

04 June 2024 2,602 5 View

Are protein models designed computationally patentable?

If we design proteins like tetrabody or triabody with unique binding sites in silico without further wet lab validation can we patent that structure and procedure?

01 June 2024 2,493 1 View

Opinions required on determination of function of hypothetical small protein?

So, I am working on a small protein (X) of Haloferax volcanii. It shows these results: 1. Mutant strain grows poorlycompared to wild type strain under low iron condition. 2. Growth of Mutant...

14 May 2024 9,037 4 View

How to start GROMACS simulation from a specific checkpoint?

My simulation suddenly stopped due to some reason. Now i cannot restart the simulation from previous checkpoint because it was not written properly. my _prev.cpt file is also corrupted....

18 April 2024 2,461 0 View

Suggest bioinformatics journals?

Please suggest bioinformatics journals which do not need wet lab experiments.

10 March 2024 2,919 6 View

How to simulate a complex at various pH on Gromacs?

We want to simulate a protein-cabohydrate complex at various pH ranging from 6.8 to 7.4. Can we do this on Gromacs?. Do we have to simulate complex at different constant pH or the system will...

05 March 2024 1,633 3 View

What protonation state will Histidine have at pH 7.4?

Histidine can adopt 3 protonation states: HIE, HID and HIP. Which protonation state will it adopt at ph 7.4

20 February 2024 8,503 0 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

How to improve plaques in Double Layer Agar Assay?

Hi all! My thesis groupmates and I are working on purifying an E. coli bacteriophage. The phage was handed down to us by the previous thesis group, but they only managed to purify it to about...

06 August 2024 5,801 4 View

Who of all the Global Scientific community will help me Prof. Dr. Yoshida make way for TPEOM, MEC ~EMC to return the atmospheric gases to the norma ?

TEP presentation caption (The Environmental Project) Re: Why should Washington’s DC, or any country government point of location think of as nowadays of as to being 'tomorrow as to come! if it...

03 August 2024 2,484 1 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

How is the bacterial genome's high protein count verified as genuine despite 800+ contigs and good metrics (98.55%completeness, 0.68% contamination)?

Given that the bacterial genome has over 800 contigs, but its quality metrics are good, with a completeness of 98.55% and a contamination of 0.68% as assessed by CheckM, what specific validation...

01 August 2024 1,514 1 View

Recovery Viurses from bacteria genome?

Hello everyone, I am currently looking for tools to recovery viral genomes from bacterial genomes, not metagenomes. However, I have only found tools that are designed for retrieving and studying...

28 July 2024 8,953 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

If my gene of interest has high GC content can it be problematic in sequencing? What kind of error is expected with GC rich gene sequences??

Gene sequencing related trouble shooting

25 July 2024 4,149 2 View

Can you visualize platelets using EVOS ?

Hi all, My lab has Thermo Scientific™ Invitrogen™ EVOS™ FL Auto 2 Imaging System, and I was wondering if I will be able to use it with whole blood, whilst focusing on platelets? The idea would...

24 July 2024 9,337 3 View

Salim Hussein Hassan

Anuraj Nayarisseri

Let me know if want to do Sequencing with Eminent Biosciences. You will have to send samples to Korea.

Vineet Singh

1. Macrogen-South Korea

2. Labgenomics-South Korea

Both above companies offer this service, and if you don't have any experience in NGS data analysis, they can do it for you.