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Questions related to Bioinformatic Tools
How can I add atomic parameters for the ions Europium (Eu3+) and Americium (Am3+)
05 October 2020 1,956 6 View
The mutations in question are variants of the SARS-CoV-2 reference genome (MN908947.3 NCBI reference) – the first isolate from Wuhan (Wuhan-Hu-1).
05 October 2020 1,695 4 View
Dear fellows, I am wondering about, how many bioinformatic tools are required to declare a variant as pathogenic and deleterious?
03 October 2020 6,685 3 View
Hello, I would really apreciate if you recommend some free and friendly bionformatic program to determine if a group of genes obtained by microarray are cancer asociated genes? Greetings and...
24 September 2020 7,650 3 View
I want to use data from TCGA available on cbioportal to perform some statistic analysis (e.g: correlation between mRNA of a certain gene and survival data, correlation between the mRNA levels of...
24 September 2020 1,253 4 View
I got LC MS/MS data of two different species of animals, How I can calculate difference in protein concentration,when I compare same protein of both species.
21 September 2020 2,397 3 View
Is there any bioinformatics tool that automatically detects the possible occurrence of any type of post-translational modification (PTM) in a given peptide PDB file or in a given peptide as a...
10 September 2020 6,589 1 View
I have 8 IV and 1 DV, they are all dichotomous and categorical data, so I am using Cross-tabulation Chi-square test. So 8 tests conducted. All test have at least one expected count less than 5. So...
30 August 2020 9,809 9 View
There are many tools to identify the protein target for a ligand. When I start with a protein, what are the best tools to figure out the possible chemical ligand for this protein?
10 August 2020 9,128 3 View
I was trying to find a plasmid origin of replication, ori-finder did not find it, and also I tried to blast against their database and try to align to other similar bacteria, but with no...
04 August 2020 5,056 8 View
We read that NK cells are CD 3- and CD 56+/CD 16+. Recently I and across two IVD approved kits from two manufacturer for lymphocyte subset assay. Kit from BD (cat no. 644611) have CD16/CD56+...
04 August 2020 9,247 5 View
I am looking for a recent diagnosis for chikungunya virus through computational biology techniques.
23 July 2020 1,096 3 View
Hello, Anybody know if adherent cells (I am using U2OS, but any general information is helpful) progress through the cell cycle when detached from the dish (I use trypsin). I want to start...
16 July 2020 9,264 4 View
Hi, I am working on molecular validation of co-expressed genes in Rice under moisture stress. I have a list of genes that are co-expressed in three rice varieties, under a particular set of...
13 July 2020 7,622 1 View
I am trying to use GPU Accerlation for GROMACS 2020.3. I have installed cuda 11.0 and my NVIDIA graphics card driver is gt-force mx130 and i am running ubuntu 20.04 but when i run the command :...
10 July 2020 8,018 4 View
I am running DIYABC for both microsatellite and mtDNA data and testing 3 scenarios. Once I start the analysis I get the following error message: "Something happened during the reftable generation...
09 July 2020 3,665 4 View
I am looking fora command that will modify 3 chains available in the original pdb into a single chain and then renumber all of the residues. I have tried using alter command but when I export the...
27 June 2020 9,127 1 View
On the Zinc15 paper 'ZINC 15−Ligand Discovery for Everyone', 38885 analogs of the Olaparib (40430143) were found as an example of chemical similarity search. I am very far from this result and...
26 June 2020 2,199 0 View
Hi everyone, I would like to ask if anyone knows any bioinformatics tool for generating a topological diagram of a protein from its 3D structure?
18 June 2020 2,213 3 View
Hi all, our collaborators would like to perform an RNAseq experiment from a 2-cell co-culture system. For this experiment they would like to co-incubate fibroblasts and macrophages from 2...
15 June 2020 6,689 3 View
I'm just learning how to perform an analysis of methylation patterns using bisulfite sequencing data, but I have some questions: 1. What database I can use for obtain bisulfite sequencing...
11 May 2020 1,271 1 View
I'm a molecular biologist, and i have a few projects coming up in transcriptomes and small RNA analysis. Can i get by without knowing any programming using user-friendly software such an Geneious...
11 May 2020 7,928 1 View
Hi everyone, I need to do MD simulation of wild type and ten variants at 50 ns. I am looking for a low-cost cloud service/ simulation environment. Would you please suggest me any? Thanks in advance.
27 April 2020 3,123 1 View
I have 56 genome sequences aligned to one reference genome sequence. Now i want to identify the number of SNPs throughout the genomes, their positions to compare between the 56 query genomes. Is...
20 April 2020 7,130 1 View