28 votes
Accepted

Why are sushi proteins called "sushi"? What are the origins of this name?

Because their shape reminded researchers of rolls of Sushi (Ichinose et al, 1990): These repeats were initially called GP-I structures because they were first identified in $\beta_2$-glycoprotein I....
Jack Aidley's user avatar
  • 6,917
10 votes
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Tips for longer fragment size and higher purity of insect DNA

Insect samples are difficult to work with primarily because they contain a bunch of polysaccharides, like chitins, that are similar enough to nucleic acids that they can co-precipitate. Standard ...
bob1's user avatar
  • 12.1k
9 votes
Accepted

What is a topological domain?

TADs were initially discovered by computing contact probabilities between regions of the genome using HiC (a chromosome conformation capture method, that try to provide an idea on how the genome is ...
ColibriIO's user avatar
  • 131
9 votes
Accepted

Biological meaning of read length

The read length has absolutely nothing to do with what you are sequencing. It is a characteristic of the sequencing technology you use. NGS sequencing techniques typically produce this sort of short ...
terdon's user avatar
  • 12.9k
8 votes
Accepted

How is the size of a gene defined?

Is there an agreed-upon definition as to how many nucleobases constitute a gene? If not, why not? There is no such definition. A gene is a region of the DNA that is transcribed. Typically a gene ...
WYSIWYG's user avatar
  • 35.6k
8 votes
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Can one identify an organism based on its genome alone?

As you specifically state: Would it be possible to systematically deduce what this organism looks like and behaves like without reference to anything else (ex: a repository of genomes of known living ...
bob1's user avatar
  • 12.1k
7 votes
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Are SNPs and alleles the same thing?

Alleles are variations of a same locus that codes for a protein (gene). These alleles can come in different forms, one of which is SNP. For example, sickle cell anemia arises from an allele of the ...
Franco Grosso's user avatar
7 votes

Where can I find SARS-CoV-2 genome sequences for the UK?

Oxford University's Bugbank project is designed to collect SARS-CoV-2 samples (and other microbial cultures) from UK Biobank participants for sequencing. Once completed this data will be available to ...
brazofuerte's user avatar
  • 1,582
6 votes
Accepted

Can both the overlapping genes (in opposite strands) produce proteins?

While overlapping antisense RNAs are quite well known, there are very few examples in which both the RNAs from the pair can code for proteins. However, it is not impossible. I can cite one validated ...
WYSIWYG's user avatar
  • 35.6k
6 votes

Why did scientists think humans had 100,000 genes (before the Human Genome Project)?

Human genome is 3.2Gbp (giga=billions of basepairs). If you assume there are 100k genes, this yields around 32kbp (kilo=thousands base pairs) per gene. Before human genome project, let's say before ...
aaaaa says reinstate Monica's user avatar
6 votes

Is it possible to deduce facts about a person's parents just by studying his/her genome?

Not the kind of complex phenotype that you describe (because nobody knows for example if/how "being abusive" is written in the genome), but yes, some things can be determined. The easiest is through ...
Mowgli's user avatar
  • 1,929
6 votes

Tips for longer fragment size and higher purity of insect DNA

I think @bob1's answer is good, and covers a lot of the bases. One thing that I think is missing however is the use of a nuclear preparation as an initial step- my understanding is that this can help ...
Maximilian Press's user avatar
5 votes

How is the size of a gene defined?

How are gene size defined? DNA is made of 4 nucleotides A,T,C and ...
Remi.b's user avatar
  • 68.1k
5 votes

Excluding the Exon, What Does the Rest of the Genome Do?

A few percent codes for RNA, like microRNA, long non coding RNA, shRNA ect. These RNA while not translated into protein do have a function. Some RNA are ribozymes, catalytically active in their own ...
JayCkat's user avatar
  • 2,926
5 votes

Which DNA elements belong to the definition of a gene?

Usually a promoter is not considered a part of the gene. Distal regulatory elements qualify even lower for being considered a part of a gene because they can regulate many genes simultaneously. ...
WYSIWYG's user avatar
  • 35.6k
5 votes
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Why did scientists think humans had 100,000 genes (before the Human Genome Project)?

There's actually no need to speculate on the answer to this question since scientists have published their estimates and methodology, as is their way. The following paper is a good review: Fields C, ...
canadianer's user avatar
  • 17.7k
5 votes

Can one identify an organism based on its genome alone?

No, current technology is nowhere near what is required to deduce the form of a species from its DNA alone without comparing it to the DNA of the same or similar species. The reason for this is that ...
Imprisoned Rhesus's user avatar
5 votes
Accepted

Transcript without a start codon in mouse genome?

The entry in ensembl has a "CDS 5' incomplete" tag http://uswest.ensembl.org/Mus_musculus/Transcript/Exons?db=core;g=ENSMUSG00000026567;r=1:165331512-165395316;t=ENSMUST00000193149
swbarnes2's user avatar
  • 5,230
5 votes
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What does ‘per DNA fragment’ mean?

They are referring to sequencing strategies where you chop a longer stretch of DNA into fragments, sequence each of these, and stitch the sequences back together. The sentence is explaining that the ...
Bryan Krause's user avatar
  • 45.7k
4 votes

How many recombination events are there per generation in humans?

"On average, between two and three crossover events occur on each pair of human chromosomes during meiotic division I" according to Molecular Biology of the Cell. 4th edition by Alberts B, Johnson A, ...
pas28's user avatar
  • 41
4 votes

Two sets of chromosome and the sequencing output

This is very similar to your previous questions, but apparently you are not understanding the explanations we are giving, so I'll try again, by giving a (hopefully not-too-technical) explanation of ...
MattDMo's user avatar
  • 15.3k
4 votes
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Actual determination of the DNA sequence in the shotgun approach?

The question appears to confuse the method of identifying and determining the order of bases in a fragment of DNA — Sanger* sequencing, Maxam–Gilbert or more modern ‘next generation’ methods — with ...
David's user avatar
  • 25.7k
4 votes

What is structural RNA?

To be very brief: A gene is a sequence of DNA or RNA, which is hereditary and has a biological function. In the Saccharomyces cerevisiae genome you posted, every gene is a DNA sequence. The function ...
Pythagyros's user avatar
4 votes

Why did scientists think humans had 100,000 genes (before the Human Genome Project)?

I don't know much about the evolution of thoughts on the subject but I would suppose that the estimate of 100,000 genes is probably caused by the one gene - one enzyme/protein ideas The one gene–...
Remi.b's user avatar
  • 68.1k
4 votes
Accepted

Is there any independent non-DNA based information system in the cell

According to the comments, the question is about inheritance systems of cells. The "mainstream" information storage and inheritance system is of course DNA (and RNA in some cases). However, there are ...
István Zachar's user avatar
4 votes
Accepted

Is it possible to distinguish between coding and template strands from the sequence?

Given a DNA sequence alone, you can annotate open reading frames (ORFs) in order to identify the coding strand, with the caveat that not all ORFs are genes. ORFs are sequence segments that begin with ...
acvill's user avatar
  • 8,296
4 votes

Genomic location-coordinate of RdRp of SARS-CoV2

A useful database and exploratory tool is the UCSC Genome Browser wuhCor1 assembly browser instance. A synonym for nsp12 is Pol. Its position range in the ...
Alex Reynolds's user avatar
4 votes
Accepted

What exactly is "chromosome topology"?

I think that there are a few things going on in this question, I'm going to try to answer the ones that I think are most pertinent: We should not expect "topology" as used in the Hi-C field ...
Maximilian Press's user avatar
4 votes
Accepted

Alternative to discontinued 10X Genomics Chromium linked-reads sequencing platform?

Maximillian provided some good information, but I thought I'd add some practical considerations: All of the long-read sequencing platforms provide quite contiguous assemblies (scaffold N50s up to ...
Kieran O'Neill's user avatar
3 votes
Accepted

How do biologists quantify "gene expression" in experiments?

The primary product of protein coding genes are mRNAs. When we talk about measuring gene expression we want to assay the steady-state levels of a specific mRNA within a cell. This is usually ...
mdperry's user avatar
  • 3,517

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