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Bioinformatics : Recent Questions and Answers (Page 8)

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

europmc and tidypmc R library for extracting or making metadata from publication

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc...

Asked on 08/30/2021

1 answer

RNASeq read coverage in protein space?

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly.I have also conducted a multiple sequence...

Asked on 08/30/2021 by CephBirk

1 answer

Ancestry of the coronavirus 2019-nCov, WuHan city, China

In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus. Can somebody assist...

Asked on 08/29/2021 by puppetsock

1 answer

Alternatives to imputation for single-cell RNA-Seq analysis to increase statistical power of DE analysis

I have a small scRNA-Seq dataset (n = 357, inhibitory neurons). This set of cells is split almost evenly between two conditions (Case and Control). I would like to test...

Asked on 08/29/2021

0 answer

Prevent Snakemake from changing wildcards: sample for every rule

EDIT: I posted this as a bug, perhaps wait for the result of that? github All, I am using Snakemake to build a pipeline. To define input...

Asked on 08/28/2021 by Freek

2 answer

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Quote:We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4...

Asked on 08/27/2021 by SurpriseDog

3 answer

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... 1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct 61...

Asked on 08/27/2021

4 answer

Comparing aligned amino acids to codon

I have a set of 4 amino acids which i have aligned,but i want to compare then with respective nucleotide sequence in terms of change codon level. I have...

Asked on 08/27/2021

1 answer

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 08/27/2021 by runeblaze

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 08/27/2021 by CodeUnsolved

1 answer

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