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Bioinformatics : Recent Questions and Answers (Page 3)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

mBED has time complexity $O(n lg n)$, claimed by Clustal Omega paper, why?

In the Clustal Omega paper, it says the following about mBED ($N$ is the number of input sequences, I assume):we use a modified version of mBed...

Asked on 12/07/2021

1 answer

Sequence alignment using BWT

My Problem: Skipping some specific background, what I want to do is judging whether some soft-clipping sequences are the same, which may result by the same SV event. Colored bases...

Asked on 12/05/2021

1 answer

differential analysis of chip-seq data

I have several sets of chip-seq data. I called the peaks using Macs2. I am pretty new to the field and I will appreciate any help. I wanted to annotate...

Asked on 12/02/2021

3 answer

Generating 3D coordinates error

I have been trying to convert a multi entry sdf file to pdb using openbabel. Everytime I check the Generate 3D coordinates box I end up with .ENT files instead...

Asked on 12/02/2021

1 answer

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform...

Asked on 12/02/2021

1 answer

Coronavirus RNA structures?

Is there anything known about the RNA structures of coronaviruses? More specifically - do they have any interesting known structures in the translatable region, like RRE of HIV or the...

Asked on 11/29/2021

1 answer

calculating nucleotide frequency per column

I have some sequences shown belowCAGGTAGCCCCGGTCAGAAGGGTTTGATTGGTGAGGCAAGTATGAACTGTATGCCTGGTAACCTATGTACTGGCTGTGAGACAGGTGGGCTCAGTGAGAGGGGTGAGTTGGGTATGTGAGGTGAGACAGGTGGAGEach line has 9 nucleotides.Consider it to be 9 columns.I want to calculate the nucleotide frequency of each nucleotide for each of the...

Asked on 11/27/2021

7 answer

Is it possible for coronavirus or SARS to be synthetic?

I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant...

Asked on 11/27/2021

1 answer

Extract sequences from partial Header

I have a library I would like to split them based on their headers. Some are related to RNA and DNA. The header contains much information, but the most important...

Asked on 11/24/2021

2 answer

Subsetting from seurat object based on orig.ident?

I am pretty new to Seurat. I want to subset from my original seurat object (BC3) meta.data based on orig.ident. however, when i use subset(), it returns with Error.ER_HER_P...

Asked on 11/24/2021

2 answer

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