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Questions related to Bioinformatics
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 6,154 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 5,955 5 View
Dear RNA-seq experts, I have a problem with RNA seq analysis, After DEG analysis using edgeR, genes that have large variation between samples are not defiend as DEGs. In my concepts, it's weird...
11 July 2019 9,169 1 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 6,592 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 7,706 5 View
Seeking recommendations on reputable providers of WSG &/or RNA-seq for a few samples, including bioinformatics of the results.
07 July 2019 7,961 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 3,747 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 4,933 4 View
What are the major factors that influence the above? Are there any good bioinformatic prediction tools for the same?
07 July 2019 989 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 9,675 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 3,569 4 View
By giving a sequence as an input, are there any available computational tools for finding the pseudogenes in a particular organism?
06 June 2019 6,737 4 View
answer .... please ??
06 June 2019 2,282 1 View
If I have a list of amino acid sequence motifs in a java regular expression format, what is the best way to identify all occurrences of these motifs in all ORFs. (I have the ORFs in a .fasta...
06 June 2019 8,278 3 View
I am doing a BLAST search using the WGS database restricted to Campylobacteriaceae but one of the times after 3h I still didn't have the results. Is it normal to take so long? Thanks
04 June 2019 1,943 2 View
hello everyone , i just like to ask the bioinformatic professionals here about the best free validation software to validate my 3D structures... i'm still new in the bioinformatic field and i'd...
05 May 2019 3,263 6 View
I would like to assess few enzyme proteins among the organism to understand the difference in their actions. The structure was modelled using homology modeling and same enzyme having different...
05 May 2019 6,586 8 View
I would like to perform positive selection analysis among mammals. I am mostly interested in positive selection in humans and I have started off with around 100 mammals species and looking for a...
05 May 2019 1,379 2 View
Hi, I have a SNP dataset containing 717045 SNPs. I want to a GWAS using Haplotype blocks. But I do not know first how to create haplotype SNP dataset for GWAS and also the criteria for creating...
05 May 2019 5,940 4 View
Hi I lysed rat hippocampi neurons and ran a western blot for B-III Tubulin protein and I saw protein bands. However, I reprobed the PVDF membrane (after three washes with TBST) with my...
18 April 2019 9,770 10 View
I have an input file containing precursor mass and peak list (m/z and Intensity) of tandem mass spectrum. The file contains multiple spectrum data. I need to identify peptide using sequest and...
04 April 2019 6,622 5 View
I'm looking for a bioinformatic server/software/tools previously described to measure the nucleosome-formation score of a given set of sequences. (i.e. workflow: input sequence -> nucleosome...
04 April 2019 8,990 1 View
What is Bioinformatics in Pathology?
04 April 2019 7,953 1 View
hi everybody, I want to use SHAPEIT2 in the my thesis for phasing. I have only a little information about bioinformatics and SHAPEIT2. I want to use freely SHAPEIT2. Best regards
04 April 2019 6,134 3 View