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Questions related to Bioinformatics
Do you know any database for searching about endemic species, their genomes, differences, DNA barcodes etc.?
11 November 2019 1,310 3 View
As nude mice still has Bcells,NK cells and DC cells. Will K562 cell lines survive in Balbc nude mice to create a xenograft model. There are very few publication who used this strategy to test...
07 November 2019 971 1 View
Hi everyone. I am newbie Phylobayes user :) I recently started running phylobayes-mpi on Cipres portal for Multilocus phylogeny with 5000+bp. Although I run my analyses with parameter...
20 October 2019 8,371 10 View
I am trying to identify enriched regions(peaks) between m6A RNA methylation RIP-seq and input data. For that, the human genome need to be split into non-overlapping 20 nt windows, then I need to...
12 October 2019 829 6 View
10 October 2019 3,815 6 View
I have bam files (3 IP and 3 input) from a RIP-seq experiment. I need to split each unique mapped reads bam file based on read strand in order to calculate then strand-specific read coverage along...
10 October 2019 7,739 3 View
I am new to the field of molecular phylogeny. I am interested in knowing the bioinformatics applicable in molecular evolution.
10 October 2019 401 3 View
Hi all, We recently started working on the COLO320 xenograft model and are trying to figure out the best time point to terminate the study for quantification of lung and liver mets? We currently...
17 September 2019 9,077 0 View
Hi, I have a list of some genes and i want to check their interaction with my target. Anyone can suggest some bioinformatic tools that can predict the interaction?. many thanks
09 September 2019 8,819 9 View
I have a very specific problem while modeling PZ (Protein Z). The protein is a molecule of 360 residues with a Gla domain (1-46), two EGFs (47-126) and an SP like domain (135-360). When looked for...
09 September 2019 9,123 7 View
Especially in public health
09 September 2019 6,121 4 View
I've got microarray transcriptomic data (from S. cerevisiae) - and I've made GO enrichment analyses - since there were many redundant GO terms I've used REVIGO for getting rid of them but I found...
09 September 2019 762 6 View
Protein on which i am working is a disordered protein and no crystal structure of this is available on PDB. I have modelled structure using I-TASSER. Out of top five models generated by I-TASSER I...
08 August 2019 5,509 9 View
I have tried to construct it using Chemsketch but unable to convert it to pdb format. I want to use glucose-2-phosphate in docking study and hence in need of 3D structure.
08 August 2019 4,251 7 View
Note - this is not about Next-gen sequencing or other major deep-sequencing projects I do a lot of simple (cheap) basic sanger sequencing of plasmids with companies like Macrogen and Genewiz....
08 August 2019 6,056 8 View
I'm trying to extract prophages from bacterial genomes, the principal issue i been having is that i have multiple hits distributed along bacterial genomes and i don't know how to extract them...
08 August 2019 5,881 5 View
I have protein protein docking complexes of some vaccine, i would like to perform MD simulation Studies of complexes using Gromacs software, Please help if anyone have standard protocol or...
07 July 2019 6,495 4 View
Hello reader; Hope so you are doing well. I have 16S RNA sequences of some bacterial species and I want to Identify glycoside hydrolases gene in those species. I want to know that is there any...
07 July 2019 7,632 5 View
Seeking recommendations on reputable providers of WSG &/or RNA-seq for a few samples, including bioinformatics of the results.
07 July 2019 7,883 7 View
Respected researchers: First i performed 10 ns simulation using gromacs and after that i calculated binding energy of complex using g_mmpbsa successfully and at this time my GPU was not ON. Then i...
07 July 2019 3,648 6 View
We know that the four native bases for DNA are AGTC, however, some of the sequences, retrieved from NCBI, contain letter 'N', which illustrates that these nucleotide bases are not deciphered...
07 July 2019 4,776 4 View
What are the major factors that influence the above? Are there any good bioinformatic prediction tools for the same?
07 July 2019 906 3 View
Hi everybody I am a Ph.D biomedical engineering student. My project is about genetic ancestry. I want to work on classification the genomes of an admixed population into different ancestries. Can...
06 June 2019 9,596 7 View
Hi Everyone, I am calculating the surface area per lipid of 200 ns membrane trajectory using MEMPLUGIN of VMD and it seems to be calculating the same too slow. Therefore, I would like to ask Is...
06 June 2019 3,473 4 View