Sorghum database, bioinformatics analysis?

Seeking Efficient Tools for Detecting Disease-Causing SNPs in Large Genomic Datasets. Any recommendations for advanced computational tools or strategies? I already used SIFT CADD MSC AlphaMissense etc and I only have the data from 7 patients and their parents. thank you for your help !!!

Please recommend any free NGS data analysis software that runs on Windows. I have downloaded and used CLC Genomics Workbench, but only for two weeks. Any other software that I can use for longer periods? 

I have been using Zeocin marker for target protein expression to verify integration in Pichia system. However, I would like to remove Zeocin marker since it's antibiotic related and not ideal for food application. Wondering what other marker gene I can use or knockout Zeocin marker from Pichia genome since the plasmid is already integrated.

Thanks for everyone!

When will the Clarivate Journal Citation Report (JCR) and Impact Factor for 2024 be released, and where (any URL) can I find them? Thanks

Dear friends! I am working on finding motifs by using MEME Suite in COX1 gene. Kindly help me.

How to proceed further?

What measures should I see for?

Since some gene prioritization tools were published in the last decade, there has been no new research in the area of gene prioritization or candidate gene discovery. Can somebody shed light on this area? Is it still relevant, or is it no longer required?

Could someone please suggest a protocol for DNA isolation for ChIP-qPCR? Additionally, between the PCI and Chelax 100 methods, which one is preferable for isolating DNA from formaldehyde-fixed chromatin?

Hi everyone,

I am trying to estimate the narrow-sens heritability of dispersal (propensity) in a natural population of lizard for wich I have a pedigree dataset. I used a bayesian approch, by fitting an animal model (function : brm ; package : brms) with three random effects (additive genetic, maternal effect, environnement). Using the posterior distribution of this effects, I was abble to estimate h² and the credibility interval, IC (function : HPDinterval ; package : coda).

My issue is that IC is very large, with the lower limit beeing very close to zero (e. g. for an estimate of h² = 0.30, IC [2e-12 ; 0.5]). How can I by sure that my estimation is robuste and that h² is different of zero ?

For now I fitted the animal model without the additive genetic effet and used loo and looic methods on both model. Comparing the output, I am sure that the additive genetic effect increase the quality of the model, help it to fitt best the data.

Is that enough ? Or do you see anything else I can do to assert / evaluate the robustness of heritability estimate ?

Thanks in advance.

Greetings everyone.

I seek guidance from individuals experienced in NanoPore sequencing of whole genomes of non-model eukaryotic organism. Our objective is to sequence the genome of an amphibian species with a sizable genome (~5 Gb) utilizing the NanoPore long-read sequencing platform. Despite employing various DNA extraction and purification methods, achieving the requisite purity for DNA extracts has proven challenging.

After numerous attempts, we have managed to produce samples that meet the quality standards set by Oxford NanoPore, with A260/A280 ratios ranging from 1.8 to 2.0 and A260/A230 ratios from 2.0 to 2.2. The DNA is not fragmented based on a simple TBE agarose gel run. We initiated library preparation with 1 microgram of input DNA, in accordance with the genomic DNA sequencing protocol using the Ligation Sequencing Kit (V.14 chemistry).

However, our sequencing results have consistently fallen short, with a read N50 value of less than 8 kb (somethimes much less) and a maximum output of 5 Gb (after 36h sequencing, load the lib. twice), significantly below our target. I am reaching out to seek insights from experienced individuals regarding potential reasons for these suboptimal outcomes and to explore strategies for improvement. Your expertise and guidance in this matter would be greatly appreciated. Thank you.

I attach an agarose gel picture with our input DNA sample (first spot). The corresponding NanoDrop purity ratios for this sample are A260/A280 - 1.854 and A260/A230 - 2.088.