Is it possible to do in silico SSR study with diploid organism genome?

More Jing Jin's questions See All

Should I include H atom into C3N5 when i am doing DFT modelling?

Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...

07 August 2024 8,414 2 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Can telekinesis, telepathy, and prediction be achieved through science?

Information in The Three Dimensions of Time.Information in The Three Dimensions of Time Information Transfer based on Brains Entanglement.Information Transfer based on Brains Entanglement Time...

28 July 2024 7,522 0 View

How to get LP fiber modes directly from Comsol?

Hi there, I'm new to modelling with comsol. I would like to ask if it is possible for comsol to output linearly polarized (LP) modes? I tried modelling a simple single mode fiber with an enlarged...

23 July 2024 4,019 3 View

Mass spectra averaging algorithm?

I am now developing a python module for ms2 database searching, would like to realize a function that similar to what Xcalibur did, choose multiple mass spectra and get an averaged spectra. But...

22 July 2024 3,975 1 View

Is it possible that the Earth's axis of rotation could change?

Due to the shifting ocean currents, the planet could be thrown off balance, altering the angle of rotation, and even causing the axis to shift, plunging us into chaos. In reality, it doesn't take...

15 July 2024 8,949 1 View

Can we calculate the CO2 adsorption capacity(mmol/g) of a solid adsorbent (MOF) using CO2_TPD analysis?

what is the relationship b/w TCD signal(a.u) and CO2 desorbed (mmol/g) ? can we plot CO2 desorbed(mmol/g) Vs Time(min) from TPD data?

15 July 2024 3,248 1 View

How to deal with lab test values above quantifiable limit?

Hi, I'm analyzing data from an oncology trial and trying to perform statistical analysis including cox regression analysis and paired t-tests. My data includes laboratory test values, including...

22 June 2024 6,181 1 View

How to cut a sample with several micrometers thick silicon oxide with DISCO DAD323 dicing machine?

I use a DISCO DAD323 dicing machine to cut my sample,which has 1-2 micrometers SIO2 on its top.However,the SIO2 is broken and fall apart everytime.I tried different cutting speed but didn't work....

20 June 2024 1,131 0 View

Does wind power turbine use increase world temperatures a lot and create hurricanes?

Wind turbines extract a lot of energy, about 30-35%, that passes through. Now they are building a lot of them, more and more powerful. Change wind trajectory is easy, if a lot of obstacles is in...

12 June 2024 9,002 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 5,138 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

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

Does post-translational protein modification cause devisions on observed pI verses calculated pI?

In running two-dimensional gel electrophoresis on bacterial protein, some spots that appear to match a protein sequence have a significantly more acidic isoelectric point than the calculated pI....

24 July 2024 8,076 3 View

Why my negative control siRNA is decreasing the target gene's expression?

Hi Everyone, I'm using an siRNA kit to knock down a target gene. The kit guarantees that the negative control doesn't target any sequence in mouse genome, and when I use BLAST I don't find any...

23 July 2024 2,673 6 View

M. Rubio

Of course, you can check the following article about Prunus species in my researchgate profile, with title:

In silico search, characterization and validation of new EST‑SSR markers in the

genus Prunus. Sorkheh et al. BMC Res Notes (2016) 9:336

DOI 10.1186/s13104-016-2143-y

Jing Jin

Hi Rubio,

Thank you for your answer. I'll definitely take a look at the paper.

Actually there are 17 published SSR markers available to me. What I am doing is trying to map those markers back to the genomes and extract those sequences. I was wondering if I can do some analysis with those sequences? For example, grouping individuals together or building a phylogenetic tree. Since I can only have one sequence from each individual genome with one marker, if the individual is a heterozygous at certain loci, is it valid to do the analysis treating it as a homozygous?

Thanks,

Jing