I am losing my mind from reading academic papers. All the papers explain the process with fancy words but none provides a clear example. At this point I think only the four Russians know how this algorithm works. And not all four of them were Russians anyway. Any help is appreciated. Thank you submitted by /u/yuogi333 [visit reddit] [comments ..read more

I am trying to make a huntingtin protein with 42 glutamine residues in exon 1. I downloaded a huntingtin protein from pdb (https://www.rcsb.org/structure/3io4). This structure has only 17 glutamine residues in its sequence and I require more than 40 glutamine residues. With the help of discovery tool i was able to make an insertion mutation in the sequence. I pasted this mutated sequence in the AlphaFold2 colab. The sequence is 1234 amino acids long. AlphaFold2 colab is aborting the process midway at "Run Prediction" stage. So as an alternative I tried Swiss Model. I got the results. But when ..read more

hi all, i’m currently writing an scRNA-seq paper focused on trajectory analysis, specifically with respect to the dynamics of transcription factors (TFs) and possible target genes over pseudotime. the easy bit is identifying TFs whose increased expression precedes that of increased or decreased target gene expression i.e., a potential regulatory relationship. i’ve been asked by reviewers to further validate these hypotheses by examining binding data to determine whether or not each TF actually regulates the putative target gene of interest. i’ve done a literature review and found evidence of ..read more

Hi everyone! I’m a wet lab scientist at a startup and have written a couple of scripts to analyze data from sequencers and bioreactors. Others want to start using these tools in their day to day, so I want to know: how can I make these tools available for non-coding folks? I wrote everything in conda environments, so my current thinking is to make a company GitHub and repos for the scripts and environment configurations. Is there a better way, though? And if GitHub is the way to go, how do you ensure people always use the most up to date versions of the code? There isn’t much infrastructure f ..read more

Hey everyone, I am quite new to RCoding and bioinformatics so would appreciate a little help! I am performing an analysis on data from the TCGA database and I have identified 9 significant lncRNAs. I have then calculated their AUC values and their sensitivity and specificity values. My AUC values are all between 0.6 - 0.62. I know a 'good' biomarker is considered to be >0.8. For one of the lncRNAs, despite having a low AUC (0.61), it has high sensitivity (0.92) and high specificity (0.96). I am a little confused how it can have a low AUC, meaning it would not be considered a 'good' biomark ..read more

I've been fighting with a ~4000 variant region to generate haplotypes for the better part of a month now. After trying pegas, GeneHapR, PopArt, and everything in between, I finally found a tutorial for PopArt that explains clearly what needs to be done to generate the proper networks. (https://www.youtube.com/watch?v=RTqT9TrbuuQ&t=484s) My question is then, for people with experience with a NEXUS haplotype file generated in DnaSP6, is it possible to edit out/select preferential haplotypes without too much trouble? I have 4095 samples in my data set for 8190 sequences, leading to ~2900 hap ..read more

Why we choose odd number for kmer value and how does it relate to canonical kmers? submitted by /u/BiggusDikkusMorocos [visit reddit] [comments ..read more

I was tryna blast TERC gene in humans and zebrafish - unable to get any results on blastn while clustal omega gives an output for the alignment. I could get results with TERT gene - did I download the wrong sequence files or what am I doing wrong? Ensembl didn't have TERC for Zf and i downloaded from NCBI - Danio rerio non-coding telomerase RNA gene, complete sequence Sequence ID: EF569636.1 Length: 317 Number of Matches: 1 and Homo sapiens telomerase RNA component (TERC), telomerase RNA Sequence ID: NR_001566.1 Length: 451 Number of Matches: 1 submitted by /u/Mendelianne [visit reddit] [com ..read more

When I submit Glide jobs from Maestro, they always run at very low priority. Assuming that I don't want to nice my other processes down, how do I make it so that Glide runs with with a higher nice value automatically? submitted by /u/balta97 [visit reddit] [comments ..read more

I'm in grad school for math and took up a math modeling for cancer class that i found interesting, since I very much see myself moving into bio and health related fields. I've got some ML and data analysis, can code in python, and do some high performance computation and parallel computing as well. I'm wondering if my mix is useful at all in bioinformatics or other bio/health/pharma related fields? Not sure if this is the exact place to ask this but I wasn't sure where else to ask? submitted by /u/responsiponsible [visit reddit] [comments ..read more