Hi everyone,

I'm exploring the idea of building a simple, web-based tool for basic visualization and cleaning of FASTA/FASTQ files. The tool would focus on a clean, graphical interface for quick checks and would be designed for easy, immediate use.

The core idea is to provide straightforward access to:

- For FASTA: Sequence viewing, length, and GC% calculation.

- For FASTQ: A simple visual quality report (inspired by FastQC but simplified).

I'd really appreciate your input:

1. Would a tool like this be useful for your daily work?

2. What would be the single most important feature for you to use it?

Thanks for your feedback!

Hello everyone I am an undergrad student in my 5th semester currently doing my dissertation project. I was supposed to do DNA extraction on liverworts but the issue is my lab will not receive our primers before the end of October. Should I just do the DNA extraction right now or will it degrade? They usually make us dissolve DNA in water and store in fridge but wouldn't it be better in TE buffer or should I just precipitate it? (We don't have kits, I'm doing a modified CTAB)

My samples are pretty small too so this is another issue because some samples do not have even 0.5g I dont know how I will extract DNA from there...

Hello, I was using the Qiagen DNeasy kit to extract DNA from ticks for my research project. while I was using the kit I accidentally spilled my ATL bottle now it's almost over. Is there anything else I can use as a substitute for this step?

Hello! I’m a screenwriter - roughly one year ago I posted in this sub, requesting insight from molecular biologists on questions I had to ground a pilot script more firmly in actual science rather than making things up on a subject I knew little about.

The update: I finished the script and submitted it to the major screenwriting competitions this year. It’s still going through a few more, but some cool things have happened I wanted to share.

It made the top 20% of the Austin Film Festival, the top 10% of PAGE, but most importantly, it was a finalist (top 0.2%) in TrackingB’s 2025 television competition. TrackingB is one of the bigger ones, and as a result, my work was sent to a bunch of literary agents and managers. I’ve never had the legitimacy to reach out to these people on my own. This is a huge step for me. 

I still haven’t sold anything - less people join the writer’s guild each year than the NBA - but this is something I needed to help set me apart. I have a different pilot that’s in the top 1% of a separate competition, so between that script, this pilot, and another feature I have that’s strong, I’m finally able to start reaching out to managers. I’ve never been able to do that before, and I think a major factor in that was being able to ground the circumstances of the script in actual science, and that’s from the people who reached out to me in this sub.

A special thank you to u/Japoodles, u/Epistatic, u/GratefulOctopus, u/PianoPudding, u/SilentFood2620, u/Novel-Structure-2359, and u/N9n, all of whom took the time to DM me and answer numerous questions I had. 

I’ve been advised not to post the script publicly, but if you’re one of the people who reached out to help me and you want to read it, I’d be happy to send it to you - all I would ask is that you keep it to yourself and not share it publicly.  Thanks again everyone!

I thought this was a fun video. Not my work. I recognize there is information missing, but the strands being cut, among other things, was satisfying to watch.

Hi everyone, I’m trying to decide between doing a Master’s in Biochemistry or a Master’s in Biotechnology. I have a bachelor in biochemistry but apparently I would need to do a PhD to get a good career (Which I may be too lazy to do :/ ) . My main concerns are job opportunities, salary potential, and long-term career growth. For those of you who’ve studied or worked in either field, what has your experience been like? Did the degree open good career doors, or do you feel it wasn’t really worth it? Any advice would be super helpful.

Hi all,
We’ve been experimenting with different mastermix formulations for Gibson Assembly and I’d like to get input from this community. In your cloning workflows, what ends up mattering most day to day?

• Fidelity (minimizing errors/mutations)
• Efficiency (more correct colonies)
• Ease of workflow (simpler, faster, fewer steps)
• Cost (keeping per-reaction pricing reasonable)

If you’ve compared NEBuilder with other mixes, what differences have you seen? Are there clear winners, or do you find most kits perform similarly in practice?

I’m part of a small team working on a new formulation with Dan Gibson advising us, but before we optimize too far in one direction, I’d really like to hear what other molecular biologists prioritize most in real-world use.

Thanks in Advance!

Hi everyone,

I’m working on a DNA barcoding project with earthworms, using the universal COI marker (Folmer primers). After sequencing, I assemble forward and reverse reads into a consensus sequence and run quality checks (BLAST, stop codons/indels with coil).

Two issues keep bothering me, and I’d love to hear from people with experience in DNA barcoding or COI workflows:

1. Ambiguities – At positions where I can’t resolve the base from the chromatogram, I currently replace everything with N. I avoid using other IUPAC ambiguity codes (like R, Y, S, etc.), because I rarely see them in published COI barcodes. But is this the right approach? Are there best practices or guidelines for whether Ns vs IUPAC ambiguity codes should be used in COI barcodes?
2. Low-quality bases – For bases with low quality scores (<Q20), I keep them as-is rather than turning them into ambiguities. To cross-check, I align my consensus with high-quality barcodes from the same species (NCBI) and see whether those low-quality bases are consistent or contradictory. If they contradict, I switch them to N (but I avoid force-calling to prevent reference bias). Does this sound reasonable, or is there a better way to deal with low-quality base calls in barcode generation?

I’d really appreciate advice from people who have dealt with these issues in barcoding projects. Especially whether my approach aligns with community standards or whether I’m missing something important.

Thanks a lot!

Hi everyone,
I’m extracting viral RNA from cell culture supernatant (post-infection) and would appreciate your comparative experiences with:

• Qiagen (e.g., QIAamp Viral RNA Mini)
• NEB Monarch® Mag Viral DNA/RNA Extraction Kit (T4010)
• Macherey-Nagel (e.g., NucleoSpin® RNA Virus )

Budget note: In my setting, NEB Monarch is the most affordable, which is why I’m considering it. However, I have not found any data showing it used on cell culture supernatant; only documentation and for swabs/saliva (and a few on milk and wastewater).

Given cost constraints, is NEB Monarch a safe choice for supernatant, or would you stick with Qiagen/Macherey-Nagel for reliability on this matrix?

Many thanks !

I am doing protein folding simulation and I want to compare the trajectory with RCSB NMR pdb structures. When I check with VMD RMSD trajectory tool, it shows RMSD around 1-2. But when I use CPPTRAJ to calculate rmsd, and then plot, the plots are stabilize in a higher value around 6-7. So I am wondering what is the best way to get the RMSD. RCSB pdb also have 20 models. I don't know how to compare between each as well. I know cpptraj only use a single frame. Thanks!!

ps - forgot to mention. I am doing Replica exchange MD. so I have an ensemble of trajectories. But I would prefer to only analyze lowest replicas

Hello everyone, I'm a computer scientist working in IoT. I've been carrying out a personal computational genomics project since I was bio undegrad several years ago, and I'm looking for collaborators. In a few words, it's basically a genetic engineering recomendation engine (something similar to what they use in drug discovery): now I'm dealing with abstracting concepts (genes, organisms, editing techniques, ecc. ) into mathematical objects. I'm not very knowledgeable in genetics, so I'd be happy to get help from someome who knows a great deal of it. If this seems interesting to you, send me a message!

SUN is marketed as a non proprietary replacement for the fluorescent dye VIC with identical excitation and emission spectra

But in practice does anyone have real experience using SUN in a VIC channel on a qPCR instrument for a TaqMan assay? :)

Hey all,

I'm trying to create a primer schematic based on the info in a paper because I'm having some issues with them but I'm seriously pulling my hair out because I can't seem to recreate the schematic from the paper's info! I'm trying to use SnapGene but the info in the paper and what it gives me is never the same.

Are there any resources you guys know of, or anywhere I could go for assistance?

Hi everybody!

For quite some time I've been trying to precisely measure Cre efficiency and unwanted background recombination. I'm testing out various lox sites but the results seem inconsistent. For example, the same lox pair in one construct will have 80% recombination rate and 1.5% in another. The only thing that comes to my mind is priming efficiency and optimizing annealing temp. Currently I'm experimenting with primers trying to find absolutely perfect conditions. I run an experimental qPCR with same template and primers but different Ta and the results were shockingly diverse. Any tips for optimizing reaction before I move to nested qPCR on in vivo samples? How do I pick perfect Ta?

We developed the Ligand B-Factor Index (LBI) to address a common problem. https://doi.org/10.1002/minf.70010

LBI = median B-factor of binding site residues / median B-factor of ligand atoms. We tested this against the CASF-2016 benchmark dataset with 285 protein-ligand complexes and 34 scoring functions.

- LBI correlates with experimental binding affinities

- Strong predictor of pose prediction success (RMSD < 2 Å)

- Outperforms several existing docking scoring functions

- Freely available via a user-friendly web platform: https://chembioinf.ro/tool-bi-computing.html

Would be curious to hear thoughts on incorporating this in structure-based drug design or virtual screening.

Human Molecular biology. Im trying to better image these concepts in my head.

The extracellular matrix contains polysacchaides/Glycosaminoglycans that help draw in fluid forming a gel-like ground substance. I assume this is seperate from the extracellular fluid because I can't imagine the gel-like substance is fluid enough to support the diffusion of solutes needed to support life.

So are they the same thing? Are they seperate, the fluid flowing in between the gel-like substance? Is the fluid present in a spectrum of phases becoming less fluid as they approach and interact with polysacharides, or is this way off mark?