Technique(s) by which the sequence of DNA is obtained. The principles are similar for [tag:rna-sequencing].

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Genome Sequencing [closed]

Is Genome sequencing used to determine the relationship between two species that are believed to have a common line of descent? How accurate is this method if so? Are there more accurate methods ...
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28 views

Walkthrough Analyzing/Processing Genotyping Data for Association Studies

I need help outlining the data analysis process of analyzing genotyping data you get back from a Next Generation Sequencing experiment. Here are the steps I currently believe you go through, but I ...
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30 views

Walkthrough Illumina Genotyping

I would love help outlining a basic walkthrough of the wet-lab techniques for processing blood samples from patients, all the way to loading a BeadChip, to the part just before Next Generation ...
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2answers
157 views

Reading and Understanding profile bands in DNA Fingerprinting

I have very limited knowledge when it comes to DNA fingerprinting. I know about the technique gel electrophoresis and how everything is carried out. But I don't know how to read the result or ...
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2answers
51 views

Blood testing for chlamydia

I am working with the bacterium Chlamydia trachomatis. The main test for this species is the naat test, which is based on amplification. But I would like to know how the bacteria affects the blood ...
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264 views

What happens after the purification step in Hi-C sequencing?

I am a statistician reading an article on Hi-C, and I am trying to better understand one of the steps in the DNA isolation and sequencing process. Since I'm a statistician, please try to avoid too ...
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332 views

How can I preserve hair or saliva for future genome sequencing?

Suppose I want to preserve myself so that I can be reproduced as best as possible, in future or be simulated in future. At the moment full human genome sequencing is a bit expensive. One could get ...
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1answer
89 views

What DNA has the most info for getting a person's likeness? [closed]

I understand that DNA can come from hair but also from other places. Let's suppose a person gets their DNA mapped by a company (there are some companies claiming to offer analysis of DNA.. e.g. maybe ...
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45 views

What would be the estimated cost sequencing?

I'm a newbie to the world of NGS, but I thought it might be a suitable and cheaper alternative to doing traditional Sanger sequencing for this particular application. However, I'm not so sure on how ...
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53 views

What is the result of modifying the reagents in the Sanger method?

If one of the dideoxynucleotides is omitted while using the Sanger method how would that affect the chain termination method of DNA sequencing?
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61 views

Interpretation of faint band for Linear Array HPV Genotyping Test

After having used the test for research it would appear as if it is very specific. What is one to make of bands that are there but faint? Or what if there are two bands and one is big and bold and the ...
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2answers
135 views

What do Illumina HiSeq/MiSeq paired end reads look like?

My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this: R1: AAAAAACCCCCC R2: GGGGGGTTTTTT Where the ...
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What is the range of “reasonable” counts of a bisulfite sequencing?

I analyzed the bisulfite sequencing data of a mouse sample (1 lane, I think) and it got enormous methylated/unmethylated counts on some chromosomes, e.g. chromosome 2. I thought it was a very a ...
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83 views

How do we know Denisovans had 46 Chromosomes

What allows sequencers to conclude that Denisovans had 46 chromosomes rather than merely knowing Denisovans had the crossover material arranged in 48 or say 44 chromosomes? See http://genetics....
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3answers
64 views

Whole Genome Sequencing and B Chromosomes

Do whole genome sequencing techniques detect B chromosomes if such chromosomes are present? My understanding is as follows: How the DNA material in a B Chromosome is mapped depends on the reference ...
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3answers
92 views

Whole Genome Sequencing and Chromosome Counts

In general, do standard whole genome sequencing techniques rely more on known chromosome counts, independently arrive at chromosome counts, and/or not directly address issues such as base number, ...
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89 views

How long is saliva viable?

Does anyone know if saliva can stay viable for about 5 days, before it gets suspended into a DNA genealogy vial for testing? Background: My brother wants to do a DNA genealogy test at a US testing ...
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40 views

Why does low sequence diversity cause sequencing problems

When sequencers are processing sequence fragments, if there is little diversity at a particular bp locus this can cause problems for the sequencer. I have the superficial understanding that when a ...
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1answer
87 views

Is sequencing error a function of the nucleotide being read?

Checking out on Google Scholar, I can see that for Illumina (just to consider one example) the sequencing error rate is of the order of 0.001-0.01 per nucleotide. Talking about sequencing error, let'...
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54 views

Is there a good analogy that illustrates the difference between early DNA sequencing techniques and shotgun sequencing?

My first university biology classes begin in September. In preparation, but increasingly out of curiosity, I've been studying some basic biology. Saying that to say, I know as much about DNA ...
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650 views

What is the strand specificity of a reference genome?

It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. So here's ...
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2answers
121 views

What is the DNA Sequence for an apple?

The title says it all. I'm just curious. I read that scientists mapped the genome for Malus Domestica, but I can't find a sequence anywhere.If this is a stupid question, I would appreciate if you tell ...
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1answer
76 views

Primer Design with Primer-BLAST over specific site

I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site. I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward ...
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1answer
133 views

View ABI chromatogram plots with python

I would like to view the chromatogram traces from a few ABI (.ab1) files. I would prefer to use python for this, or a function with python bindings, or at least some open source package such as EMBOSS....
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35 views

Is 100% accuracy in DNA sequencing possible?

I would like to obtain a complete genome of a canine (with mitochondrial DNA too) at 100% accuracy. Is it even possible with the current technology? The source I have is potential degraded, i.e. dried ...
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112 views

Design arbitrary degenerate primers (with non-binding criteria)

I would like to design a number of arbitrary degenerate primers (primers with variable bases, e.g. NGATWGCTSATNGC) for a TAIL-PCR. I would like to be able to ...
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83 views

What does the “cov” mean in a velvet assembler generated contig name?

A exmaple of a contig name generated by velvet assembler: NODE_127_length_39203_cov_244.873016 What does cov_244.873016 mean? ...
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Why do many DNA solutions contain additional compounds?

DNA solubility data in only water is scarce. A previous question asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple ...
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162 views

Which pair of primers should be used to amplify the ORF in PCR? [closed]

So I want to choose the correct set of pair of primers to amplify the ORF of the gene that corresponds to amino acids in a protein. The start and stop codons are underlined. (I know that these need to ...
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35 views

How to be a Noah-esque biopirate and store the genes of every plant and animal [closed]

Preamble. Please criticize this idea. It is too romantic to be possible. All of the news about the sixth extinction got me thinking about it. Thanks The price of DNA sequencing for humans has ...
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3answers
71 views

Patterns/Motifs Repository [closed]

I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching). I am curious about the "regular expression (regex)" (pattern/motif) ...
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156 views

Different names in paired-end sequence files

I am aligning paired end sequence reads using bwa mem and I get an error saying that ...
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1answer
149 views

How do carrier RNAs increase yield in sequencing experiments?

I would like to know how carrier RNAs increase yield in RNA/DNA sequencing experiments. Is their main function in the precipitation steps of each protocol (i.e. small quantities are difficult to ...
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1answer
45 views

X-recessive disorders and genetic markers

Please observe the following pedigree of a family with a x-recessive disease (bleeder disease). The A's are genetic markers so close to the disease gene that recombination is negligible. I ...
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74 views

Write the haplotypes of the family

I'm doing old exam assignments to prepare for my finals on Monday and I've stumbled on one assignment that I'm not sure how to tackle. A family with 2 children is examined for cataracts using PCR ...
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270 views

What is a genetic marker?

In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and ...
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863 views

What is the difference between sequence, reads, and contigs of genetic material?

Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example? I am new to bioinformatics, and I have not found any conclusive ...
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Does blood typing still provide a use for ancient tissue analysis?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be ...
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207 views

Is Sanger sequencing still used in labs, and therefore worth learning?

If iI were to have access to funds for research, would learning this technique be a boon for me? Or are next-gen sequencing methods all the range now? My knowledge of both are limited.
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Trying to understand the big picture behind DNA sequencing, alignment and searching

I'm about to start a bioinformatics research project but I haven't any biological background. I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like ...
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43 views

What does a read simulator do?

There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software
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54 views

How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and ...
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2answers
112 views

Primer Design With Primer-BLAST

I am trying to design primers for sanger sequencing snp detection. In the past I have used Primer-BLAST, but I'm trying to pick up KRAS codon 12 mutations. The problem is that in Primer-BLAST you ...
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1answer
74 views

Reliability of Sanger sequencing

Hailed as the "gold standard" of sequencing, I was wondering to what Sanger sequencing owes its incredible accuracy to. If possible, I would like a quantification of the accuracy (because I doubt it ...
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2answers
276 views

How can we create a living dinosaur using DNA technology?

I'm wondering what would we need to do to create a living dinosaur using DNA technology? If it is not possible with current technology, will it ever be feasible? In the movie Jurassic Park, ...
2
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2answers
129 views

Help reading chromatogram

A genetic variation is found in this chromatogram: It says that the "reference sequence" is the top line and that I can use the general genetic code to find the reading frame. I can see that there ...
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53 views

Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
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1answer
322 views

Why is it harder to sequence plant genomes than animal genomes?

Plants seem to be less complex organisms than animals, but despite that there are less plant genomes sequenced. Is that because plant genomes are more complex, for example in terms of regulatory ...
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3answers
84 views

DIY storing family DNAs' samples for future uses (eg medical)

I have a question I could not get an understandable reply from Google and I am no expert in the matter, so my plead to you is if you could give me practical and relatively easy to follow advice. With ...
4
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1answer
151 views

DNA sequencing problem

First off, let me start by outlining the problem: Your laboratory has established a technique for examining DNA replication in a cellular extract. To the cellular protein extract, you add nucleotides,...