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30

Think about it like this. Suppose you own a hundred copies of "The Lord of the Rings", a 500000 word novel. Unfortunately, you have those hundred copies in the form of several million tiny scraps of paper, each of which contains about ten sequential words from the novel. Your task is to take those several million scraps of paper and put them in order so that ...


28

Computers are used in several steps of sequencing, from the raw data to finished sequence (or not): Image processing Modern sequencers usually use fluorescent labelling of DNA fragments in solution. The fluorescence encodes the different base types. To achieve high throughput, millions or billions of sequencing reactions are performed in parallel in ...


18

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 ...


9

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

Short Answer In a nutshell, DNA sequencing technology has a limit to how long a stretch of DNA it can read in one go. Long Answer So what most commonly occurs is the length of DNA you wish to sequence needs to be (almost randomly) chopped up into given lengths (depending on the technology) and each length or read is sequenced in parallel. But now you ...


8

This difference would have the greatest impact on treatment for cancer, in which a treatment protocol is based on genes deleted, amplified, altered in the tumor vs the reference genome for that patient. In terms of health risks based on SNP genotypes, the data are far from complete. Sure, some level of risk can be assigned to a variant (SNP), say at certain ...


8

Perhaps you can draw inspiration from classic paper on lambda cloning: Maniatis T, Hardison RC, Lacy E, Lauer J, O’Connell C, Quon D, Sim GK, Efstratiadis A. 1978. The isolation of structural genes from libraries of eucaryotic DNA. Cell 15: 687–701. Try selecting tissues from the animal which you think is "enriched" (i.e. highly expressed) for the specific ...


8

I think this is due to the over-representation of recognition sites with length 6: data<-c(16, 16, 12, 12, 6, 6, 6, 6, 4, 16, 6, 6, 6, 6, 15, 15, 6, 6, 6, 6, 11, 11, 6, 6, 4, 4, 6, 6, 11, 12, 6, 6, 23, 23, 6, 6, 6, 6, 9, 12, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 10, 10, 6, 4, 6, 6, 11, 11, 9, 9, 6, 6, 6, 6, 5, 5, 8, 8, 6, 6, 8, 8, 6, 9, 10, 10, 6, 6, 6, ...


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

All sequencing methods, be it classical Sanger sequencing or next-generation sequencing (or even third generation) need a certain amount of DNA to work with. You either need to extract DNA from a large-ish tissue sample or you need to amplify DNA content from a smaller sample. The first approach is often impractical, or downright impossible (when you want ...


8

After reading the paper cited I think the logic goes like this: DNAse I will create free ends at accessible sites in the genome. However shearing during subsequent DNA isolation is also a source of free ends, and these represent noise in the analysis. You have to put in a lot of energy to shear DNA to very small fragments, so I infer that mild shearing ...


8

IMPORTANT EDIT : In your particular case, if you are working with bacterial genes, splicing is not an issue since bacteria do not have introns. I am leaving the information here since it may be useful to someone else. However, I recommend you focus on the UTRs since they are probably what is causing you problems. There are three things that could be ...


8

Every nucleotide sequence has six possible reading frames, because each codon (determining one amino acid) consists of a base triplet (3 frames), and there is a complementary strand which could be coding (3 reverse frames). To find the possible open reading frames contained in your sequence, you have to look for start codons. That is: ATG. But, as said the ...


8

There are several nucleotide sequence datbases available. One of the largest is the NCBI GenBank at http://www.ncbi.nlm.nih.gov/genbank/ You may use the search bar at the top to search for nucleotide sequences belonging to a certain organism or gene. For example, searching for "E coli" will give you the full genome sequences for several bacterial species, ...


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

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

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

It's just a "string" where nucleotides encode something but I have no idea what they encode specifically. It sounds like you are describing a computer program, represented by a string of bytes on the hard drive. Unfortunately, the analogy breaks down very quickly because DNA is vastly more complex and a lot of aspects are still poorly understood. But ...


6

In a genome, there are usually billions of base pairs. However, it's impossible to read all of them in one go. The DNA is fragmented, and the sequence of the fragments is determined. Next-generation sequencing techniques are faster and cheaper, but produce only short fragments (say, 100 base pairs, this depends on the technology). It's extremely ...


6

The question is not too broad, just involves a fair bit of work to both do the research and compose a response. I'll do the latter, but in brief. The strings of the four nucleotides encode genes. Sometimes these genes are broken into protein-coding portions (exons) and sometimes intervening, non-coding regions (introns). Bacteria, for example do not have ...


6

Another list of simple human traits can be found on the Western Kentucky University site. I will ask also AB0 and Rh Blood Groups, you can use this also to check associations with other genotypes/phenotypes, see this stackexchange question If you are going to sequence also the mitochondrial DNA, you may want to reflect on questions to ask also about their ...


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

Note that the query sequence you have provided matches the minus strand of your target sequence. That means not only that the target sequence will be reversed (as you have noted), but it will also be complemented as well. So in the GenBank record, you should not look for the sequence CCGACCGA... starting at position 10835, you should look for the sequence ...


5

23andMe is a company that provides sequencing. Before they sequence your genome, they ask you to fill in a couple of surveys, one of which is about your physical features. Here is a list of some of the questions they ask: How much hair do you have on your upper/lower back? When you walk, in what direction do your feet naturally face? Do you have ...


5

If the organism uses an alternative code, the predicted protein sequences would always include the same type of amino acid substitution errors. This pattern should become apparent when you compare the proteins to other organisms. In reality, the most common alternative code uses UGA for tryptophan instead of the usual stop. If you make the mistake of using ...


5

Here is the approach I ended up using, in part thanks to all the contributions here. The associated R script is below or can be downloaded from: BOLDS SEQUENCE RECOVERY This creates 999 unique sequence files in plain text, with each sequence being identified to species level and few species being found across more than one sequence. It also creates the ...


5

There are a couple key words in this question - anonymous and teaching. Yes, NCBI is a source for sequence data, but it is not anonymous (it is annotated, which means a student could also find it and copy/paste that annotation without doing the actual analysis). Notice, I am not assuming that the request is for human data. Now, if anonymous human data are ...


5

Not sure why Larry Parnell was down-voted, he was not technically wrong. Crystal structures of the most popular restriction enzymes are already known and can easily be found the Protein Data Bank or Wikipedia for graphical reference. Any stretch of double-stranded DNA makes a complete 360 rotation (about it's helical axis) in 10-10.5 base pairs. A 180 ...


5

As you mentioned in the question, current sequencing platforms split the genomic DNA into many small pieces which the machine then analyzes. The product of a sequencing experiment is millions or even billions of short "reads"---strings of A, C, G, and T representing the nucleotides of a single fragment of DNA. The DNA reads in this form aren't particularly ...


5

I'm not an expert on Shannon-Weaver Index, but according to wikipedia it is the same as exponentially transformed Renyi entropy. If it is the case, you can compare them since they are scale invariant summary statistics. If you want error bars, you can always try resampling methods such as bootstrapping. Hypothesis testing can also be done with bootstrapping, ...



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