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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...

## 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...

## 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...

## 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...

## 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...

## 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...

## 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...

## 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...

## 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...

## 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...