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

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79 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
22 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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0answers
22 views

Genome sequencing (DNA) [closed]

Given the current state of technology to create many copies of DNA segments, how many copies must be made (the depth) to get the probability of error to be astronomically small. No worse error rate, ...
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0answers
27 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 ...
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1answer
24 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 ...
2
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1answer
40 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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1answer
27 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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2answers
77 views

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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1answer
22 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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0answers
26 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
43 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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0answers
32 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 ...
2
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1answer
33 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
27 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 ...
2
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0answers
37 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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3answers
84 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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2answers
233 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 ...
2
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0answers
25 views

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 ...
6
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2answers
66 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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0answers
6 views

Why low variant frequency in exomeseq data (ANNOVAR)?

I've got an annotated ANNOVAR file with 300.000 nucleotide variants of 4 genomes. There's one thing I don't understand when looking at the data: Why are the variant frequencies so low in comparison to ...
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2answers
76 views

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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1answer
34 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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0answers
25 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
53 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
27 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 ...
2
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2answers
120 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
38 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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0answers
39 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
86 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
70 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
72 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 ...
4
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2answers
229 views

explanation of meaning of high-throughput

Almost all of the papers about bioinformatics, I faced with the high-throughput word, but I could not find any explanation about it (I think it is so easy to understand and thats why anyone explains ...
4
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2answers
109 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
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0answers
20 views

EMBOSS matcher and supermatcher - incongruent results?

I am trying to align a sequence to the mouse genome. I know a priori that part of my sequence should align to chromosome 9, but not all of it. I gathered that EMBOSS' ...
6
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1answer
48 views

Has the protein composition (with identification) in honey and other honeybee byproducts been studied?

I am interested in studying honey and other honeybee byproducts. I have not been able to find sequence or structure records for any of the contents of honey. In particular, I want to study the ...
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2answers
40 views

How do I find a protein from this DNA sequence?

I have a DNA sequence from a sequencer. How can I determine what protein is it? I tried some translator but it didn't help. What protein is this and how can I determine it? The sequence: ...
2
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0answers
20 views

Inter-codon mutations statistical analysis

I am looking for a statistical approach to inter-codon mutations. For example a 64*64 (64*63 actually) table, that contain the possibility of mutation from one codon to another codon (CCA to CAA or ...
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0answers
69 views

Miseq loading with low concentration library

I have made a DNA library for miseq using truseq pcr-free dna HT kit (550bp insert). The problem is that at the end of library preparation and pooling, I need at least 2nM of library for denaturation. ...
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0answers
34 views

Superpatients for Cancer resistance

I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer. The article is ...
6
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1answer
120 views

Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?

My understanding is that PCR is carried out until a fluorescent nucleotide halts replication. The segments of DNA are fed through the capillary tube based on size, sifting through the segments from ...
4
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1answer
107 views

Does DNA analysis allow determining amount of chromosomes?

Nowadays it is possible to sequence the DNA of extinct species, such as the Neanderthals, the Denisovans, and others. Is it possible to determine, solely from the sequenced DNA or from known bone ...
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2answers
45 views

During bridge amplification of DNA sequences, why aren't sequences amplified in both orientations?

During bridge amplification, when sequences attached to adapters on the surface form "bridges" and are replicated, it seems like sequences with either end attached to the surface will be created. For ...
3
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1answer
34 views

Gene Sequencing and Plasmapper

Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)? For information I would like to convey that I am using Plasmapper and BioJava for achieving ...
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1answer
66 views

Simplest Biological Organism? [duplicate]

What is the simplest biological organism from which a DNA sample has been or could be obtained? Could the resulting DNA be processed and examined in such a way that the resulting information would ...
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5answers
1k views

How can I find a complete human genome file

I'm trying to figure out how I can download a file that represents the complete human DNA sequence. I don't care too much about the format – I'm able to write C++ code to parse it. FASTA seems like a ...
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0answers
32 views

What is the meaning of this poor sequencing result?

What is the meaning of this poor sequencing result? What is the problem? Can anyone guide me, please. Thank you.
2
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1answer
30 views

Transcription rate expressed in microarray per hour

This article gives measurement of transcription rate and the unit they're using is microarray per hour. For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...
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2answers
57 views

where to find the relative frequency distribution of synonymous codons

Most amino acids can be encoded by more than one codon. For example, Serine can be encoded by any one of ...
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0answers
58 views

What good is the MinION?

This year, Oxford Nanopore MinION has been shipped to some researchers for testing. The advantage of a table-top sequencer for diagnostics and personalized medicine is obvious. Similarly, research ...
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1answer
699 views

What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...