17 votes
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Publicly available genome sequence database for viruses?

There area few different influenza virus database resources: The Influenza Research Database (IRD) (a.k.a FluDB - based upon URL) A NIAID Bioinformatics Resource Center or BRC which highly curates ...
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10 votes
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What is deep sequencing?

I found a post useful for this topic. It explains the difference of coverage and depth. It also has a useful explanation on how to calculate coverage and depth. Here is a copy of what the link says ...
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  • 216
10 votes

Why does the SARS-Cov2 genome has letter t

We sequence and therefore typically report assemblies as DNA sequences, even if they're actually RNA.
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  • 19.2k
9 votes

What is deep sequencing?

There are several questions in your post I'll try to answer each one: Is there any way to calculate how deep the sequencing is ? See gringer's answer. TLDR: The depth of the sequencing is how many ...
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  • 4,602
8 votes

What is deep sequencing?

Sequencing depth is typically calculated as the number of total bases sequenced divided by the number of bases in the target genome. An Illumina sequencing run with 2x125 bp reads and 500 million read ...
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  • 11.7k
8 votes

How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?

It seems to be explained right there in the image you posted: So, the three strains were classified based on three specific variants: Strain S, variant ORF8-L84S: a variant in the gene "ORF8&...
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  • 8,121
7 votes
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What does the yellow mean in this image from Virus Pathogen Resource?

Sulfur atoms are shown in yellow. The molecular viewer that you use is JSMol (JMol ported to the web). Atoms are colored by element: grey C, blue N, red O and yellow S. If you wonder how other atoms ...
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  • 1,091
6 votes

Frequency of specific viral sequence in .BAM or .fastq

Most read aligners will report unaligned reads as well, which presumably will include your viral sequences. I would ask them to formally confirm that the BAM files will contain unaligned reads before ...
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5 votes

Economist article on coronavirus

R is a reference to R0, otherwise known as the basic reproductive rate, and means the number of new cases from a single patient infection. R0 has to be above 1 for a disease to persist. It is a ...
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  • 7,339
5 votes

Algorithmic investigation of viral proteins for vaccine design

There isn't a vaccine for any coronavirus, and your question is generally about targeted attentuation, which is a complex area. The basic building blocks for any vaccine development is virological ...
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  • 7,339
5 votes

Understanding some of the computational bottlenecks of Covid-19 research

I can only speak of drug design (and even then I am terrible at turning down the jargon). In the case of drug design, this is pretty much plan C. Namely, none of compounds that entered clinical trial ...
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  • 3,529
4 votes

Which sequence alignment tools support codon alignment?

I don't know of any transcript-to-transcript aligners that are able to do this, but LAST can align transcript queries to protein reference sequences using a specified frameshift cost. Here's the ...
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  • 11.7k
4 votes

Publicly available genome sequence database for viruses?

In addition to what others have suggested, I would also recommend PaVE as a resource. This is a curated database maintained by the NIAID and current holds over 300 papilloma virus genomes.
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  • 255
4 votes

Viral genome assembly using broad viral ngs pipeline?

Since you are already using the Broad Tools sets you can use Picard FastqToSam to make the conversion As far a clipDb I am unfamiliar with that and a quick google search and look at the trimmomatic ...
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  • 2,556
4 votes
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Calculating the mortality rate of a pandemic, e.g. coronavirus 2019-nCov?

This may not strike most as a bioinformatics, but getting the key clinical outcome is essential in understanding the molecular basis of pathogenicity. I think the mortality rate is over-reported. ...
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  • 7,339
4 votes

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

The evolutionary related group (clade) of betacoronaviruses you have identified share an amino acid homology of 85% and include SARS. I know this from the underlying tree published on BioRxiv of a ...
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  • 7,339
4 votes
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Are the conclusions in "The proximal origin of SARS-CoV-2" legit?

In summary, the authors are saying the complete opposite of "human intervention". While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses ...
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  • 7,339
4 votes

Calling for one specific SNP from multiple sequencing runs

Getting SNPs from whole-genome data is usually done via mapping sequencing reads on the reference (bwa-mem or bowtie are two popular mappers) and then using one of variant calling tools (like ...
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  • 5,287
4 votes

Consensus sequence from vcf file

Making a consensus sequence tends to involve some arbitrary decisions. In this case, the common practices are: Use the ancestral allele (this isn't always apparent) Use the most common allele ...
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  • 19.2k
3 votes

Practical use of RNA structure

Please look up flavivirus 'double loops' as you described them previously (post for "Coronavirus RNA') and associated RNA secondary structure anomalies for dengue virus and associated vaccine (...
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  • 7,339
3 votes

Economist article on coronavirus

R, the reproductive number, relates to the average number of (new) people that will get sick (infected) per person that is already sick. For instance, if $R=2$ and you start with a single infected ...
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3 votes

Frequency of specific viral sequence in .BAM or .fastq

If you are interested in a particular viral sequence, it seems wasteful to request bams that are aligned to the human genome, but you could request bams aligned to the human genome with unaligned ...
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  • 724
3 votes

Coronavirus RNA structures?

To add a more complete answer: the current coronavirus is closely related to the SARS virus that caused the outbreak in 2004, and on which much research has been done. Here is a general review of the ...
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3 votes

Why is there a chloride ion in this 3D model?

It is a crystallisation artefact. Namely, the protein are placed in a condition where they fall out of solution without aggregating a gloop (as happens in most well in xstal trial) and to pack as a ...
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  • 3,529
3 votes

Understanding the fasta File Format

Your understanding of FASTA format is about right. The type of basic problem you're eluding to we term "sequence alignment"- edit distance might be okay for teaching but in practise we use ...
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  • 3,462
3 votes

Virus genome: protein inside another protein

Note that the protein sequence of ORF8b is not contained within the protein sequence of protein N. That means that they are translated from different frames (though they are in the same orientation). ...
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3 votes
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>My counter is counting genotypic combination occurences more than once, how do I ensure it counts one combination and doesnt count it again?

Alright, so there are a number of problematic patterns in your code - as far as I understand what you are trying to do. Next time, try to post a reproducible example that people can use and more ...
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3 votes
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Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

A comment from a Nextclade's user satisfies my actual needs, I will post it here for future reference: Hi - one possible source is the metadata file for UCSC’s daily-updated tree of public SARS-CoV-2 ...
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  • 2,644
3 votes
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Visualization of mutations in (part of) viral genome - existing tools?

I ended up using lolliplots from the trackViewer R package; it can do VCF-based visualization and is flexible enough I can feed it data from other sources (I wound ...
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2 votes

Which sequence alignment tools support codon alignment?

Try MACSE v2 (https://academic.oup.com/mbe/article/35/10/2582/5079334) will align multiple protein-coding nucleotide sequences based on their amino acid translation while allowing for the occurrence ...
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