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Questions related to Bioinformatic Tools
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 4,937 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 6,929 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 4,773 3 View
I want to understand the basics of docking, and also know about all bioinformatics tools which are free of coast and helpfull in in-silico analysis?
23 February 2021 9,029 2 View
Dear everyone, When I using the rda function in r, I met this question. As you can see in the figure, there are a lot of deep blue points which refers to the species. But I would like remain...
16 February 2021 9,215 2 View
There is some confusion as to where factor 8 is stored, older text books say that they are stored in alpha granules but none of the recent literature mention this. I alsohave read that they are...
16 February 2021 1,532 1 View
I know there are bioinformatic tools that allow epitope prediction to determine if a certain peptide would trigger an immune response. I also read that for allergen diagnoses IgE of sensitised...
10 February 2021 4,300 3 View
Hello everyone, How are you guys doing? I'm currently working with antimicrobial peptide (AMP) project and one of our objectives is to predict the interaction of peptide against bacterial cell...
02 February 2021 1,452 3 View
I am trying to measure telomere length in an ant species using the TRF method, which is a Southern blot technique. Currently, I am struggling with analyzing the images and would appreciate any...
30 January 2021 763 3 View
Except PASS, by using PASS, we can predict biological activities.. Any other tools?
13 January 2021 7,284 1 View
Hi everyone, I am using the pyTMs plug in on Pymol to phosphorylate a particular threonine in my protein. I am having difficulty in selecting only one or two residues - it seems I can only...
06 January 2021 484 3 View
I am checking the synergies between two antifungals and a standard protocol is given by CLSI M26-A document, but i cannot access it. Anyone with a solution or other references kindly share with...
31 December 2020 6,007 1 View
Dear All, I have the data of metabolic pathways in case and control, well there are pathways which are represented several times due to the involvement of reactions in case, well now I would...
10 December 2020 4,647 5 View
I have constructed some polymer structures using Material Studio. But I need LAMMPS input files for the simulation constructed from the Material Studio. Does anyone know how to get lammps input...
09 December 2020 369 1 View
#autodock #virtualscreening Question1: Am I doing this right , means do setting up conda on server works for virtual screening (AUTODOCK)? Question2: How can I modify the script (submit4.py)...
07 December 2020 2,642 3 View
I am interested in the different tools that can be used to create custom databases for targeted sequencing and how to trim the databases based on the amplicon size? Also, should custom databases...
03 December 2020 3,243 3 View
I am searching for new antimicrobial peptides and I don't have many skills in bioinformatics, so I want to know how to use these software packages to identify candidate coding regions within...
02 December 2020 8,551 4 View
Dear All We have revealed good results of certain fungal against cercaria of schistsoma. No we are seeking a good online tool, or any other methods to predict the extent of interaction between...
13 November 2020 9,843 1 View
I'm trying to build local gene synteny to identify homologs between different species. To do that, I've been accessing each individual gene of interest, going into gene view in NCBI and...
05 November 2020 9,188 2 View
Hello, I need to draw figure exactly like the ones below? Is there software that can do that for me? Even if not the same design, just the same idea. I can edit their design by myself. Reference:...
27 October 2020 1,489 3 View
I have a set of about 1000 homologous protein sequences with high diversity across various genera and families. What I need is to perform BLAST alignment of each possible sequence pair and obtain...
26 October 2020 1,332 5 View
Looking for tools with proved accuracy to detect ploidy levels in microbial whole-genomes.
15 October 2020 4,411 3 View
Hello, I am working on drawing a phylogenetic tree with samples sharing some somatic mutations. The basic process of my work is similar to this article. Population dynamics of normal human blood...
15 October 2020 8,182 4 View
the 2nd protein is of particular interest as it have two forms. their is an experimental hypothesis that its one form can lead to its self degradation in vitro taking it down from bound complex...
06 October 2020 8,440 1 View