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21

The short answer is that corn genome is large and has a huge amount of duplication events. Around 80% of the genome are repeated. It's hard to assemble genomes with large amount of duplications because our sequencing technology, practically, at best can give ~500 base pairs. Figuring out the ordering of duplicated regions relies on scaffold sequences or ...


10

What a timely question. Does DNA contain information beyond protein synthesis? Yes. In fact, protein-coding genes only constitute a tiny part – less than 2% – of the whole DNA. There are of course many other genes which aren’t protein coding: there are genes for ribosomal RNA and we find more and more genes which code for small RNAs, such as tRNA. But ...


10

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 ...


9

You might be interested in the INK4A locus (chromosome 9p), encoding both p19 and p16 genes, very close to p15. You can read a description here. All three proteins are known experimentally to exist. Now, whether these are two different genes or the same gene with alternative splicing and start sites leading to different reading frames it's up to ...


9

A human genome sequence can uncover large deletions and insertions in the genome and would give the genotypes of both common and private (rare to very rare) small polymorphisms (e.g. SNPs) and SSRs (simple sequence repeats). From this information, one can learn about some curiosity traits (say, sensing asparagus metabolites in the urine, slow or fast twitch ...


9

Okay, I'll take this out of the comments and put in an answer for all of us to work on. To directly answer your question: "Is there an estimate for the percentage of these genes whose primary function is related to regulation of gene expression?" It depends on how you define "gene expression." And what cellular processes you want to include in ...


9

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

The sequencing technologies that were developed in the last 20 years have a range of optimal use at an average A+T/G+C rate. Both highly AT-rich and GC-rich regions are complicated to process by the different sequencing technologies. Each technology has different ranges of usage, but to name one, Illumina technology prefers sequences in the middle range. If ...


8

This question drops firmly into the lap of molecular evolution and the constraints that are placed upon genes by the forces of mutation, selection, drift and recombination. There are numerous situations, particularly gene duplication, that can result in a gene that is free from the selective constraints of it's parent, many of which will accumulate so many ...


8

The human genome contains less than 416 base pairs, so, even after including a factor of 2 for the two strands and another to allow for some genetic variation, there must certainly exist some 17-base string not found in either strand of the genome. Now, 417 bits is two gigabytes, which fits easily within the memory of a typical desktop computer these days, ...


7

Why was decoding the genome so significant? Because decoding the genome gives us a complete picture of the genetic makeup of an organism. What made it so difficult? The repetitive sequences as mentioned by other people is a main problem. Imaging you are trying to complete a big puzzle with millions of pieces. Each piece represents a sequencing reads that we ...


7

In short, yes, it is possible. There are companies that sequence part of your genome and then can trace it back to your ancestors. All human family trees can be traced back to their African origin 200 000 years ago, but the companies that sequence your genes do not do that. For example, 23andMe sequences only 1 million of your base pairs (single nucleotide ...


7

Take a look at the strategies used to sequence the wheat genome. Wheat is hexaploid. The project is described at http://www.wheatgenome.org/. For early work on the maize genome, we employed methyl filtration in order to reduce genome complexity and size - transposons are filtered out and genes + promoters and such remain. The gene sequences are different ...


7

Yes, look at FANTOM and their work. There are about 2000 transcription factors and co-factors in the human genome. These are proteins, of course. If you add a couple (or few?) thousand microRNAs and a few dozen anti-sense transcripts, although small in size, you inch that percentage upwards. With some 70% of the human genome transcribed, by some estimates, ...


7

Insects and spiders have tremendous sexual dimorphism, with males often being much smaller than females. They are pretty much just sperm carriers and sometimes do not eat. Insects may have two or one sex chromosome, where males my have only one chromosome. As is pointed out in the comments, not all mantis' species display this dimorphism. Since such ...


7

If the anti-sense transcript is correctly annotated and in the databases (a very very big if), then it will have a different name. For example, the mouse Msx1 anti-sense transcript has the RefSeq accession NR_027920 while the sense transcript of the same gene is NM_010835. In general, each transcript that is transcribed from a given locus has a different ...


7

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 ...


7

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 ...


6

I can't comment on how A+T richness complicates the sequencing process itself, but I can comment on complications that arise when annotating the sequence. Ab initio gene predictors are often based on hidden Markov models that are very sensitive to base composition in the genome (di-nucleotides, tri-nucleotides, etc). These gene finders typically perform very ...


6

The larger differences are most likely in epigenetic marks on the DNA. The environment is a lot different today than it was 2000 years ago and those differences are stronger determinants of epigenetic change than sequence change. 2000 years is only about 40 generations and that is not very much to see great differences in DNA sequence or allele frequencies ...


6

I've had a little encounter with this question in the past few months so I'm updating here... The overall answer is 'really a lot about some things, but not as much as you'd like to think about others.' There is a scientific genome interpretation 'contest' that has been going on for the past few years called CAGI (Critical Assessment of Genome ...


6

You bring up a good point. "Coding" is a term that obviously carries some historical baggage that is gradually becoming less and less relevant. "Coding DNA" has typically been used to refer to DNA that encodes one or more functional protein products, which are constructed from an mRNA intermediate. As we've been learning over the last several years (and as ...


6

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 ...


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

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 ...


5

Well - a lot if you knew what questions to ask... The most obvious thing is sex: if you can find the x and/or y chromosomes. Other things like skin color, eye color, etc, or hereditary diseases and all that would involve running the genome through some sort of database which had values for both pheno and genotypes so you could correlate some of those ...


5

The Karr et al. paper attempts to capture most of the details in their model by combining features from the genome, transcriptome, proteome, and metabolome. This work heavily builds off of the coarse-grained models that you ask of especially on the work from Bernhard Palsson from which Markus Covert did his training. The answer to your question rests ...


5

In the literature, there are examples of DNA analysis from very old specimen. For instance, look at the analysis of both nuclear and mitochondrial DNA from 62 buried humans exhumed from a Mongolian cemetery dating from 2,000 years ago, as described by Keyser-Traqui et al. 2003, Am J Hum Genet 73(2): 247–260. Despite, the publication is open-access, the DNA ...


5

Part of the increase in power to detect a genetic association via GWAS-genotyping comes from long haplotypes. Many dog breeds went through selective breeding bottlenecks 100-200 years ago. Many lab model organisms, such as flies, worms and plants, have recombinant inbred lines that aid in GWAS discovery as well. The price one pays for this increased power, ...


5

Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though: General, text search, useful if you have a gene description (as in the case described in ...



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