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There are no perfect resources for this information in the public domain quite yet. However, there are three that are making really good progress. The first is mycancergenome at Vanderbilt. They were one of the first resources to put this type of information on the web. They tend to be pretty stringent in the level of evidence and type of aberrations that go ...


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I'm going to say the same thing as @Serine but in a slightly different context. Let's take an example where you want to compare smoking persons against non-smokers. In this context, you'd want to take a DNA sequence of smoking persons. However, due to technology limitation you won't get a single DNA sequence from the sequencing machine. You'll get millions ...


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My understanding of those three words as follows: sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are DNA/RNA or aa sequences reads are just a short hand for sequenced reads. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example ...


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Sanger sequencing is still used in the labs today - and not only on the side. Next-generation sequencing has its strength when it comes to sequencing very large amounts of DNA (basically whole genomes or exomes). Sanger sequencing is used when you want to sequence smaller regions or portions of a genome/plasmid. Typical read length is (depeding on the ...


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No its not Depends on the scale you are workin on The dideoxy termination method of DNA sequencing (often called Sanger sequencing after the technique’s inventor, Fred Sanger) has been the workhorse of pretty much every molecular biology lab for the last 30 years. However, over the last few years the method has been increasingly supplanted by ...


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You could store DNA diluted in water at -20C for a very long time. The only problem with at home storage would be the type of freezer most households have. These come standard with defrosting feature, which thaws up the freezer to remove the ice accumulation... This would affect the stability of the DNA at long term scale. Having a styrofoam box to protect ...


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If you have access to a laboratory (or at the very least a centrifuge and pipettes) and some laboratory experience you can extract the DNA from the cells which would be much easier to store. There are a number of commercial DNA extraction kits available that are easy to find on google and order online. I don't want to promote any particular brand but I've ...


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RAM's answer is very good, I'll just add on the computational side, short reads are error prone. That's important to account for when aligning or assembling. The reads themselves can just be inaccurate, which we detect by having multiple reads overlapping by a lot; we assume that stray discrepancies seen in only a single read at a position are errors. ...


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Here's a quick summary of a few mis-hits in your otherwise good analysis: Not many bioinformatics applications use Hadoop, Apache Spark or Apache Flink. In fact, I have never heard of the Apache Spark and Flink tools, and I've seen only 2 people use Hadoop to process alignment files. Reads are not "converted" real, physical DNA. They are representations ...


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In general, a read simulator does the following: Selects regions from a reference sequence with some sort of predefined or user-specified size distribution. Converts the sequence from those regions into single or paired end reads with quality scores. The quality scores and read lengths are typically user defined. Introduces errors into the aforementioned ...



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