28

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. More recently, they have been called short consensus repeats or sushi structures because of their shape.


13

The difference boils down to UnTranslated Regions. A CDS or coding sequence is the part of a transcript that is actually translated into protein. Therefore a CDS will (almost) always start with an AUG codon and stop at one of the three STOP codons (UAA,UGA,UAG). The transcript however (note that I am referring to mature transcripts that have already been ...


11

Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one. Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further ...


11

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 but he won the prize for making specific sequences of RNA bases which were then fed to cells, resulting in specific amino acid chains, which ultimately deciphered ...


10

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/GrCH38 from 2013, which are the most current genome assembly). Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have ...


10

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 pairs because mutations do no only change one nucleotide to another (what we call a substitution) but sometimes add or delete few (or sometimes many) nucleotides. ...


9

You're asking about the C-value enigma, in particular this kind of diagram:1 The quick answer is that there is no "why" in evolution; things happen and if they're beneficial they tend to stick around more than the deleterious things. The longer, (slightly) more satisfying answer is non-coding DNA. Thanks to non-coding DNA the size of a genome doesn't even ...


9

Top 10 long processed transcripts in humans (with multiple isoforms), from gencode 19 annotations: Transcript Length(bases) ------------------------ TTN-018 108861 <-- Titin TTN-019 103988 TTN-002 101206 KCNQ1OT1-001 91666 TTN-201 82413 TTN-202 82212 TTN-003 81838 MUC16-001 43732 ...


9

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 organized inside the nucleus by computing the probability of each contact to be located nearby another locus). People have found that instead of being random, ...


9

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 read you're seeing. The read length does not change because you are sequencing a longer molecule. You would still get ~250nt reads even if you were sequencing an ...


8

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 heterozygotes at this SNP-position.


8

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 beak development. What they did in this paper was to inhibit in chick embryos two signalling pathways (which are actually conserved amongst all animals, not ...


8

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 should have a transcription start site dictated by a promoter and a transcription stop site marked by termination signals (like terminators and poly-A signal etc.) ...


7

Your question could be phrased more specifically to avoid ambiguity, but rephrasing it the way that I suspect you mean it, ("Is there any evidence showing that [the rate of] copy number variation changes over time?"), then yes, there is indeed. The rate depends on many factors including which mechanism and which organism and which region of the organism's ...


7

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.


6

Probably development, in particular transcriptional regulation. To quote each link in turn, They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry ...


6

In theory it's possible to have an approximation, but not to know with certainty. Identical twins have the same genomes and look very much alike. Whether it can be done in practice depends on how well we can model the relationship between genes and looks and on how much information is necessary for a judge to permit arresting and questioning a suspect. ...


6

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 100kb for the full length isoform. See either the Wikipedia article or the one linked below for more details: The complete gene sequence of titin, expression of ...


6

Humans generally have similar nucleotide counts, but they are not often going to be exactly the same. What allows for this variation is multiply determined, but here are some ideas. The neutralist hypothesis states that most genetic change is not subject to selection [1], and this is especially evident in humans where there is a lot of junk DNA outside of ...


6

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 1990, people were isolating a lot of genes from human-derived tissues. You can use google scholar to find relevant papers. From quick search, you can see that ...


6

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 sex chromosomes. For example: if you look at the X chromosome of a man, you can tell for sure that it comes from his mother (because the Y can only come from ...


6

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 researchers through the UK Biobank: We originally developed this system as a pilot study to determine the feasibility of prospective microbiological culture ...


5

Excellent question. The answer is that, in general, there is a higher rate of mutation in spermatogenesis compared to oogenesis. This is because there are more cell divisions during spermatogenesis, which allows for opportunities for mutation. In addition, repeat diseases like Huntington’s sometimes have a phenomenon known as anticipation. This is when the ...


5

A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident) coverage. Edit by dd3: In the cases where "a new gene is discovered", i.e. genome reannotation, it is ...


5

In GWA studies you tend to analyze your "lead" SNPs in regions where genotypes are correlated (known as linkage disequilibrium). If you find an association between another SNP with the outcome, and this SNP is correlated with the original variant, you can perform a conditional analysis where you adjust for the original SNP in the model. This is to test if ...


5

Operons, often but not always, contain clusters of genes (under the control of an operator region) which are involved in the same metabolic pathway. There have been several theories for how these groups of genes have arisen but the current feeling seems to be based around the regulation of the genes in question 1. To facilitate co-ordinated gene regulation ...


5

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 number of genes in the human genome. See here for their press release with a lot of information. Additionally these two articles are as well interesting, if you ...


5

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, some people have 10 repeats of CTTT, others have 11, others have 12 etc. The largest of those fragments, at its maximum length, are about 350 base pairs. The US ...


5

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 replace Python with C or Java and eventually replace R by Python or Julia, I find Bash to be really necessary. To compare Python to R, Python is much faster. ...


5

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 example: RU2S (DCDC2) and RU2AS (KAAG1) pair. While RU2S is constitutively and ubiquitously expressed, RU2AS is specifically expressed in kidney, bladder, liver,...


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