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Questions related to Bioinformatic Tools
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 5,108 3 View
Hello everyone, I'm building an homology model of a nicotinic receptor, but there are missing residues in the intracellular domain (dotted line in figure) which lead to strange spaghetti like...
16 August 2021 9,798 5 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 3,681 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 2,780 3 View
to detect particular mutation and the effect of drug on T or B lymphocyte population
21 July 2021 394 2 View
I am trying to sequence a gene with degenerate primers. The partial sequence which I got is showing 89.5% identity with other sequences (gene of interest) in Blast. When I am doing MSA in NCBI it...
14 July 2021 6,555 3 View
I've been working with HEK293T cell line for the last 3 months and over the last month, they seem to keep dying after a week. I restore the cell line from stocks frozen in liquid nitrogen and...
05 July 2021 2,438 3 View
Hello guys! I did some ab-initio modelling using Rosetta's de novo prediction protocol (...
01 July 2021 8,287 0 View
In solar energy bankabilty studies, is the geometric mean of statistic metrics an acceptable indicator for model overall perfomance?
29 June 2021 3,247 7 View
Hi What is the best R package for QTL MAPPING in a large population?
28 June 2021 6,512 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 3,494 3 View
To obtain the moment of inertia values of my compounds, I performed calculation using gaussian 09 program (B3LYP/6-31+G(d) level of theory). In the log file, however, the values I want to obtain...
25 June 2021 5,673 1 View
In molecular docking how can I find an unknown ligand attached to receptor and remove it using Pymol ? Please suggest a technique to identify/ remove any other macromolecule attached to it.
10 June 2021 1,394 5 View
We are trying to isolate cf-DNA from urine to no avail. Anyone with an in-house protocol that works?
01 June 2021 3,214 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 9,436 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 1,012 6 View
I am looking for the residues of a protein that normally become masked to exclude them as possible phosphorylation sites. There aren't any models yet built for this protein so I was wondering if a...
13 April 2021 7,268 1 View
I am using PyRx0.8 in automated molecular docking and I encountered an error shown in the pictures attached below. The protein receptor won't set as an Autodock macromolecule because there are...
10 April 2021 1,575 0 View
The sample is highly degraded and the stereo microscopic images indicated a honeycomb appearance with minute spines in the coenostrum. The calice widths are about 1-2 mm. I'm having doubts with...
08 March 2021 7,578 4 View
I'm optimising a protocol for coral mucus sampling and DNA extraction for 16S rRNA gene sequencing. There are many different methods described in papers, mainly by syringes or swabs and different...
04 March 2021 2,140 5 View
I must search for HEK-293, HEK-293T and so on type cells proteome. I need to find endogenous expressed proteins (e.g. cells not transformed). In my case, I would like to find if these cells are...
04 March 2021 1,986 0 View
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
03 March 2021 5,374 4 View
During a computational analysis, I found that for a protein of a plant, two different subcellular localizations are seen using CELLO and WoLF PSORT. For example, in CELLO, it identified the...
02 March 2021 7,179 2 View
I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...
01 March 2021 5,031 3 View