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Questions related to Bioinformatic Tools
In the description of a dataset in proteome exchange, one of the modifications is monohydroxylated residue. what is it? is it a fixed modification or variable modification?
30 August 2022 9,113 0 View
Hello, I am a student studying stem cell engineering. I am going to stain human stem cell-derived chondrocytes with Alcian Blue staining technique. I differentiated mesenchymal stem cells using...
13 July 2022 2,132 0 View
Hello, I'm havaing difficulty understanding the relationship between crystalline properties and mechanical properties of polymers. I'm compounding two biodegradable semi-crystalline polymer 1) PLA...
16 June 2022 8,942 3 View
Dear all I would like to model a miRNA-mRNA duplex 3D in pdb format using prediction tools. I have used viennaRNA package by RNAfold using the following command "$ RNAcofold -p --noGU
06 March 2022 7,822 0 View
I knocked down a gene in human neural progenitor derived neurons for a neurosphere migration assay. I found that the KD neurons migrated longer distance than WT neurons. However, when I knockout...
04 March 2022 8,730 0 View
Hi, I have just started using snapgene and have downloaded a plasmid sequence off addgene to have a play with. Addgene says a gene is under control of a KasOp promoter, but when I insert the...
11 February 2022 1,312 1 View
Systems biology is a discipline to understand not how an individual’s function but how complexity systems (many interacting parts) in biology works. It Involves very precise measurement of...
07 February 2022 5,578 3 View
Many research articles have removed the 3rd codon positions in PCGs and rRNA genes for the Phylogenetic tree construction.
03 February 2022 3,761 2 View
Hi there, I want to analyze deferentially gene expression of mice before and after treatment. I have 6 mice and "paired-end" sequences, so how I could merge all my "before treatment" data to...
22 January 2022 3,555 6 View
Hello everybody, Recently we faced a problem with emerging red leaf spots on fiddle-leaf fig (Ficus lyrata) plants (as shown in the attached picture) under the greenhouse conditions (25 °C, 50%...
21 January 2022 1,522 7 View
I recently did a western blot of a secretory protein, the result shows that the size of this protein in cell lysate is smaller then it in culture supernatant. Is this normal? Do some people have...
24 December 2021 7,385 5 View
Hi everyone, I want to prepare a sodium phosphate buffer of 0.02 M (pH 7 and 7.8). Could you help me, please? I want to prepare this solution by using di-sodium hydrogen phosphate dihydrate...
11 December 2021 9,148 3 View
Missing residues in Schrödinger's Prime homology model.
19 October 2021 4,942 3 View
There are many visualisation software and their mechanism are more different from each other. The visualisation technique is important for my research.
29 September 2021 3,137 13 View
Can anyone help me with protocol for removing host DNA contamination from phage lysate. Any protocol by using silica gel matrix for removal of host DNA
24 September 2021 1,751 4 View
I need to check the ligand-receptor interaction on the Discovery studio analyzer or another software but I have separate PDB files. I tried to merge the ligand (which is in a protein format) and...
14 September 2021 8,235 6 View
Given that the DNA barcoding is not an effective tool to delineate interspecific divergence but intraspecific divergence between coral species (Shearer and Koffroth,2008), how accurate is the...
11 September 2021 5,034 3 View
Using pymol to visualize cyclic peptide. The cartoon representation of cyclic peptide is missing at the head to tail linkage which when represented with line and stick representation is...
05 August 2021 3,606 2 View
I need to know in what situation, those alignment types should be used? And why? If you know any related article or reference please let me know.
26 July 2021 2,690 3 View
Hello guys! I did some ab-initio modelling using Rosetta's de novo prediction protocol (...
01 July 2021 8,191 0 View
Hi What is the best R package for QTL MAPPING in a large population?
28 June 2021 6,427 4 View
We just recently assembled a genome of a plant and would want to use Circos to draw the circular map comparing it with another genome. The genome has been annotated using MAKER-P. The final...
26 June 2021 3,405 3 View
Hello I want to make input files for Amber package to run molecular dynamics simulation. I don`t know how can i find references for choosing Histidine protonation state and N- and C- terminal...
30 May 2021 9,358 2 View
I have obtained a publicly available GWAS summary data which contain column such as chromosome: position (for SNPs), effect allele, reference allele, beta, se, P-value. I need the rs ID of all the...
23 April 2021 943 6 View