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Questions related to Bioinformatic Tools
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 6,608 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 9,820 9 View
The expected peak is around 470bp, but the second peak appears in 900bp and 1100bp. Sequencing result was
18 August 2020 8,599 0 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 9,147 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 5,079 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 9,265 5 View
I am looking for a recent diagnosis for chikungunya virus through computational biology techniques.
23 July 2020 1,123 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 9,278 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 7,649 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 8,031 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 3,707 4 View
Hello, I'm trying to figure out if there's contamination in my DNA samples which affects my sequencing results. Here's the nanodrop data: Sample
02 July 2020 9,027 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 9,153 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 2,206 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 2,230 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 6,698 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 1,297 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 7,944 1 View
Easy to input a linear peptide sequence in the pep-fold server and get the result but how to input the same sequence in N to C terminus cyclization and get the possible cyclic peptide structure?
08 May 2020 9,539 0 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 3,139 1 View
I have searched on PDB but I didn't succeed in retrieve ACE 2 from PDB. Does there any option to obtain this Enzyme.?
21 April 2020 1,327 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 7,254 1 View
I need help regarding In Silico Vaccine Design for Multiple Epitope Construct.
18 April 2020 4,936 0 View
We have a patient-derived antibody that we are characterizing. We know it is binding to SOMETHING in skin cells by our western blot, immunofluorescence, and dissociation assays, but we don't know...
14 April 2020 4,284 0 View