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Questions related to Bioinformatic Tools
Hi all, I'm trying to use PWMs for a transcription factor of interest to identify conserved binding sites in upstream promoters (up to 5 kb from TSS), across several vertebrate species. My model...
05 May 2019 2,755 1 View
I have a list of genes that have been proven to be up-regulated in a human disease condition of interest. I also have a protein which according to literature is said to be a DNA binding protein. I...
05 May 2019 3,173 2 View
I would like to understand using bioinformatic tools if a peptide interacts with a protein, how can I do it?
05 May 2019 8,554 4 View
I would lilke to predict possible interactions between costimulatory molecules expressed by dendritic cells with naive T-cells using bioinformatic tools, but I don't know that whether it is...
05 May 2019 1,870 1 View
Hello everyone! I have a question on heatmaps with a cladogram (like the one shown in the picture, taken from...
05 May 2019 3,474 2 View
I have annotated several genome sequences with their proteins, this is available as either a .faa Protein FASTA file of the translated CDS sequences or a .tsv of the protein annotations (outputted...
05 May 2019 5,535 2 View
I want to check whether any response element is present for a particular set of transcription factors on my gene of interest. I have already found EPD (http://epd.epfl.ch/) for promoter sequence...
05 May 2019 1,199 7 View
I want to analyze ligand-protein interaction (3D) with bioinformatics tools, please give recommendation about reliable software or web service. Thanks.
05 May 2019 1,050 5 View
The value of M defines if a population has undergone recent reduction. There is another term called as critical M or Mc apart from M. What does it mean and how it is related to M. Thanks
04 May 2019 606 0 View
I am looking to validate the information generated from metagenomic sequencing. I know that I can carry out qPCR to validate my data. And I guess Random forest regression analysis can be done too....
23 April 2019 4,587 1 View
Hello everyone, we are characterizing some proteins in the context of vaccine development and we are interested in determining there are any epitopes that may rather lead to immune evasion. Don't...
04 April 2019 3,040 3 View
04 April 2019 7,221 1 View
I’ve used the same normalization and chip to search a gene expression in R2 Genomics Analysis and Visualization Plataform, but I have compared very different cells (like lung cancer and melanoma)....
04 April 2019 7,073 1 View
i want study cancer genome by bioinformatics tools. can advice me in articles or review paper can guide me to do my research.
04 April 2019 5,109 5 View
I’ve read an article where authors analysed some gene expression using MeV and they said that the ”datasets were normalized by the average expression across all samples”. Then, they have used...
04 April 2019 1,658 0 View
I am working on single nucleotide polymorphism studies in Formalin fixed tissues , i want to know how i can find out my selected SNP'S whether its a Germline or somatic?? is there any online...
04 April 2019 1,572 5 View
I performed a large scale methylation analysis by RRBS-Seq on Infinium Human Methylation 450K BeadChip platform with generated raw data in FASTQ format. What are the main steps to do the...
04 April 2019 6,335 4 View
I am aware that TGF-beta (in combination with IL-6) can promote Th17 (and Treg) differentiation, while inhibiting Th1 and Th2. Yet, I wonder if Th17 can produce this cytokine at steady state...
03 April 2019 4,767 3 View
I am dealing with a predicted 40 kDa MAP kinase in WB. I don't have access to LC/MS to make sure of its MW, so I rely on that of the strongest band detected (I'm not worried about faint ones...
27 March 2019 5,849 2 View
hi, I am trying to pull down methyl rich genomic regions using MedIP, but my negetive control ( igG ) shows equivalent enrichment as test. I isolate genomic dna, sonicate it using diagenode...
25 March 2019 973 1 View
Hello together, do you have some advice for a optimal GFP sequence for an expression in E. coli BL21 (DE3)? I want to create an Insert sequence including a SUMO protein in combination with a His...
14 March 2019 8,516 1 View
I have a 16S rRNA gene sequence of a bacteria. I wish to identify the organism with the help of phylogeny tree. I tried different alignments such as CLUSTALW and MUSCLE for multiple sequence...
13 March 2019 5,270 5 View
After running cufflink for two samples of RNA-Seq data, I used cuffmerge and executed the following command cuffmerge -o -g -s assemblies.txt Where assemblies.txt contains the...
12 March 2019 689 3 View
Hello! I'm developing a Pharmacophore, and trying to mutate some residues in my receptor but I keep getting an error in Desmond Module I dont know if it is my computer or something else If someone...
06 March 2019 778 1 View