28 votes
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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....
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  • 6,771
11 votes
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How were the first primers made?

The MIT synthetic chemist Gobind Khorana won the 1968 Nobel Prize in Chemistry for his work which successfully was able to make chains of Ribonucleic acids. The chemistry was difficult at the time ...
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10 votes
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What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

Lets state what a Mutation is first. Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/...
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10 votes
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Are the number of base pairs in a given chromosome same between different individuals?

Welcome to Biology.SE. if I take an X-chromosome from two random humans would I count exactly 155,270,560 base pairs in both cases No, you would probably not find the exact same number of base ...
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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 ...
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  • 6,328
9 votes
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What's the longest transcript known?

Top 10 long processed transcripts in humans (with multiple isoforms), from gencode 19 annotations: ...
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  • 35k
9 votes
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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 ...
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  • 131
9 votes
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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 ...
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8 votes
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What if a Point Mutation is seen in only half the coverage for its location?

I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have homozygotes and ...
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  • 2,889
8 votes
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How many dinosaur genes are in a chicken genome?

Be careful when reading media as they tend to exaggerate. That Abzhanov paper is interesting; it will be better when it's published and the figures released. He does a lot of evo-devo work surrounding ...
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8 votes
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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 ...
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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 ...
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  • 6,328
7 votes
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What is the genomic position of HLA-B*1502 variation?

HLA-B*1502 is not a SNP ID but rather, a name of an allele of HLA-B. This allele is made up of multiple mutations which can be found here.
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  • 751
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 ...
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  • 1,552
6 votes

What's the longest transcript known?

I think a good candidate is the human titin gene. The gene itself has 363 exons, depending on the isoform it has between 27.000 and 34.000 residues. This makes up a processed mRNA length of up to ...
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6 votes
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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 ...
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6 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 ...
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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 ...
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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 ...
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  • 1,883
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 ...
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5 votes
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How many different protein coding genes are in the Human Biome?

The Human Microbiome Project collected samples as shown in the image below from healthy volunteers: They give an estimate of about 8 Million genes in the human microbiome, which is about 360x the ...
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5 votes

Is there a known minimal stretch of DNA that can distinguish any two people in the world?

Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, ...
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  • 1,120
5 votes

What are the programming languages important to learn for a geneticist or bioinformatician?

Comparing some commonly used languages in bioinformatics I think that indeed Perl is losing users but there are still quite a lot of people using it. Bash (or other shell) is essential. While one can ...
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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 ...
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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 ...
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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. ...
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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, ...
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  • 17.5k
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 ...
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5 votes
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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
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  • 4,680
4 votes

How were the first primers made?

The process of sequencing was, and can be, assisted by cloning a DNA fragment into a known site in a plasmid designed to help sequencing. That cloning site is flanked by a known sequence(s) that can ...
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