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Questions related to Bioinformatic Tools
What are the bioinformatic tools that can be used to detect the N and C terminals of protein?
11 April 2020 9,237 2 View
I am reading the following paper. I had a hard time to understand CPMG and CEST and the difference between them. Is there anyone who can explain to me please Structure and Dynamics of an...
10 April 2020 8,457 2 View
Hi, I want to know how efficient are the new metagenomic content prediction tools such as PICRUSt and Piphillin in predicting functions and dynamics ( such as the presence of other genes) using...
07 April 2020 3,782 0 View
I actually have two queries. Biochemical studies suggested presence of an enzyme in an organism but the gene encoding the enzyme is not known. I would like to find out gene candidates based on...
01 April 2020 3,450 2 View
I am developing an algorithm to predict protein complex and I want to measure the GO enrichment for all the predicted complexes which tool should I use to do such analysis for all predicted...
31 March 2020 279 3 View
Hi, I'm a new user of Autodock Vina. I have a problem when validating a docking method for protein-ligand (organic compound). Can anyone explain to me, step by step, how to get a good RMSD...
30 March 2020 1,072 3 View
I have used BLASTp and InterPro to identify the proteins in a new species of bacteriophage, which has given putative identification to roughly half. What are other ways I can identify more of the...
25 March 2020 6,879 3 View
I am able to obtain multiple vcf files detecting mutations in individuals. Each person has similar chromosomal but different mutation. I want to merge all these output files to either a csv or...
22 March 2020 1,679 6 View
Does anyone know how to increase the ring thickness when generating BLAST Ring Image Generator plots? Thank you so much in advance!
19 March 2020 8,315 3 View
Dear fellow Researchers, I am currently trying to analyze Affymetrix microarray data through dChip software and I have the input files - probe sequence and CDF for Rat 230 2, yet facing issues in...
09 March 2020 7,784 3 View
Hello, I am trying to run the pipeline MiR-PREFeR I have run the command pipeline and I have this error after the "Done sam2bam" I have this error : Error occurred when filtering regions and...
05 March 2020 6,075 3 View
I have already used Frodock 2.0 online bioinformatic tool for docking the protein protein complex. However, unable to download and visualize the output pdb. file by using PyMOL software. Why is...
03 March 2020 9,509 2 View
Genome editing (also called gene editing) is a group of technologies that give scientists the ability to change an organism's DNA. These technologies allow genetic material to be added, removed,...
03 March 2020 10,031 3 View
I'm relatively new to bioinformatics tools and need to look at biosynthetic gene clusters, someone suggested using antiSMASH but I have no experience of this software. Can anyone suggest any tips...
25 February 2020 8,537 3 View
Dear All, Based on ORCA conserved regions, CpG islands, and histone methylation, I predict a putative promotor for my gene of interest with one of my colleague's help. I need to find/predict...
22 February 2020 3,181 3 View
Prediction of enzymatic activity based on common genetic variation.
20 February 2020 6,714 2 View
Hi, Typically, the solvent accessibility of water-soluble protein is computed by using a water molecule with a size of 1.4 Å). For my research work, I need to compute the relative lipid (-CH2 as a...
15 February 2020 486 8 View
I am trying to run the pamlX for CODEML but somehow not able to get start the run option. After loading all three files that are .ctl, .phy, and .tree, the pamlX program stands still and the RUN...
14 February 2020 5,142 2 View
The current Legionella pneumophila SBT databse ( http://bioinformatics.phe.org.uk/legionella/legionella_sbt/php/sbt_homepage.php / http://www.ewgli.org/ ) maintaint by Public Health England’s...
14 February 2020 882 8 View
Hi everyone! I've been study the expression of 5 microRNAs using TaqMan assays in several cell lines (microRNAs were selected through literature review) and I obtained statistically significant...
13 February 2020 2,833 4 View
Hello everybody, I am new with the meta-analysis in Genome Wide Data so I have this doubt. I have read METAL documentation, which is by far the most used meta-analysis software in both EWAS and...
13 February 2020 3,012 3 View
1. There are several database containing nifH sequences like fungene (19500 seq), arb database (32,954 seq), zehr (72000 seq) and farnelid (5,00,000 seq). what is the difference between these...
11 February 2020 450 3 View
Hi everyone, if I do not use spike-in RNA isoform controls for a customized RNA sequencing experiment (not the whole transcriptome, just based on few specific genes we are interesting), so is...
09 February 2020 7,310 2 View
Hi, Can someone please help me with the elution step for performing two-step chromatin immunoprecipitation? I intend to do this experiment using two different epitopes (V5 and Myc) and pull down...
07 February 2020 9,918 0 View