The process in which the DNA base pair sequence of all or part of an organisms genome is obtained.
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23 views
Reverse complement of reconstruction model for assembling reads
One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
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0answers
20 views
What is the purpose of Y-shaped adapters in Illumina sequencing?
Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.
The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.
...
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1answer
49 views
Why is Sanger sequencing inferior for detecting SNPs in cancer cells?
I am familiar with Sanger sequencing, but at the level of an undergraduate. A lecturer of mine tried to describe Sanger sequencing as losing the sequence information in noise when used to detect ...
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1answer
23 views
What is solid-phase bridge amplification?
During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?
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1answer
45 views
What's the difference between shotgun sequencing and clone based sequencing?
What are the main differences between shotgun sequencing and clone based sequencing?
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2answers
104 views
BLAST DNA Sequences Reversed
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:
It looks like it's ...
3
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1answer
69 views
Results of a complete DNA sequencing - are they 100% reusable?
Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)?
After that is done, it the complete genome can be stored and once the new genes (and they ...
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3answers
105 views
Separating DNA Fragments by Gel Electrophoresis. Are all the strands for one size the same?
My apologies if my question is too basic, and please point me to a more appropriate forum. I am reading the textbook "Essential Cell Biology" by Alberts et al, and am consulting other sources as ...
4
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3answers
89 views
Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?
I have a vector sequence and would like to find the following nucleotide sequence in it.
AASYWSRA
This query sequence uses several degenerate symbols, defined ...
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1answer
48 views
Free/cheap DNA sequencing options for developing countries? [closed]
I would like to know what are the options for an average person in a developing country to get access to this technology, and be able to get their genome sequenced.
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1answer
46 views
How are geneticists able to isolate gene functions?
As an example, this Scientific American article describes a known area in the dog genome that metabolizes carbohydrates.
How is it that researchers are able to determine specific functions such as ...
3
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0answers
27 views
Sequencing rtPCR product
So I have a validated set of primers for rtPCR from Biorad that contains SYBR green. If I do rtPCR, can I use the rtPCR product after purifying it with a Qiagen PCR purification kit? Also, I'm under ...
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1answer
67 views
Number of reading frames in nucleotide sequence
In class of molecular biology was posed this question:
"How many reading frames start in sequence of nucleotides 5' ... ATATGAATGATGACAT... 3' ?"
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3answers
75 views
What are the limitations of commercial-grade DNA genotyping compared to full sequencing?
I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what ...
6
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2answers
178 views
Finding proteins in DNA sequence
I have to do a task for a university task and I need to understand some things
before figuring out how to do it.
The task is the following:
Find matches of known proteins (DNA-PolyI,II,III) to ...
9
votes
2answers
282 views
What is the difference between SOLiD, 454, and Illumina next-gen sequencing?
I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in ...
1
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0answers
24 views
Minimal information about [blank] guidelines
The MIBBI and other organizations compile create dozens of "Minimal information about..." guidelines to guide meta-data creation for experimental datasets. These guidelines could/should be adapted to ...
3
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0answers
59 views
Comparative cost of RNA-seq vs sequencing full length cDNAs
I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
8
votes
1answer
285 views
Digital Genomic Footprinting for ENCODE
I'm reading over the ENCODE Nature papers, and one of the papers referred to is "Global mapping of protein-DNA interactions in vivo by digital" by Hesselberth et al[1].
Genomic footprinting is a ...
3
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0answers
48 views
Cheapest Way to Measure Germ Density
I would like to measure the surface density of Staphylococcus bacteria and Rhinoviruses (only those two, to be specific) within my home. What's the cheapest way?
The textbook procedure is to:
rub ...
7
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1answer
50 views
Sequence of ribosomal RNA
Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli, ...
5
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1answer
105 views
Is there a detectable amount of bacterial DNA in the blood of infected persons?
With which bacterial infection in humans has it been shown that bacterial DNA can be found in the blood?
If any is found it is likely not to be very much, and even difficult to distinguish from ...
4
votes
2answers
89 views
Sequencing from PCR
As far as I understand it, PCR can be used to make many copies of one gene. My question is, is it possible to sequence DNA after PCR and is it easier than sequencing it via other methods. If it is ...
4
votes
1answer
93 views
Is it possible to sequence only the 16S rRNA component? If so, how?
There have recently been several papers on using 16S rRNA as a way of identifying species (here, and here). I'm wondering if it's possible to sequence either just that subunit of the ribosome or just ...
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0answers
54 views
bam viewer that works on authenticated ftp urls with username/password combination? [closed]
Are there any BAM file viewers that will work on authenticated ftp urls with username/password combination?
For example, something like this:
...
11
votes
4answers
190 views
Why did high A+T content create problems for the Plasmoduim falciparum genome project?
The main paper for the Plasmodium palciparum genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply ...
6
votes
1answer
373 views
ChIP-seq vs ChIP-exo
I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.
As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
5
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2answers
129 views
Can I compare Shannon indices of metagenome gene data?
I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the ...
8
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2answers
83 views
Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping?
There are several companies (most notably 23andMe) providing SNP genotyping for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it ...
6
votes
3answers
188 views
What's the use of DNA sequencing results?
Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA "string" - the sequence of nucleotides.
What's the use of that? It's just a "string" where nucleotides encode ...
20
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4answers
758 views
What exactly are computers used for in DNA sequencing?
I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing.
There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts.
...
11
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2answers
139 views
Why are there N's after Sanger sequencing?
After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence. I know the N's mean that the computer can't tell what the base pair is, but why is ...
6
votes
1answer
78 views
Mechanics of going from DNA sequence to metabolic network
My apologies for possibly a naive question. I'm a statistics type and have been asked to assist with analysis of metabolic pathways (and networks). However, I would like to have at least a layman's ...
10
votes
2answers
130 views
protocol for pulldown of DNA breakpoints?
Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination ...
7
votes
1answer
288 views
How to clone and sequence a gene transcript of unknown sequence?
How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA ...
4
votes
3answers
94 views
How to create a collection of anonymous sequences for teaching and testing? [closed]
I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection.
The sequence files would be used for teaching and for testing ...
10
votes
3answers
382 views
Why do restriction enzymes tend to have an even number of bases in their recognition site?
When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases.
I wondered if this was just a co-incidence, so I took the data from this ...
12
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4answers
326 views
Questions to ask to a panel of people that will be sequenced
Some genes have been shown to be associated with left-handedness.
Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are "right or ...
10
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1answer
297 views
Sequencing the genomes of polyploid organisms
I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about ...
11
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1answer
188 views
What are the limitations to current nucleotide sequencing technologies?
Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...
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0answers
43 views
How are whole Haplotypes for Sequencing isolated?
Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered ...
11
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1answer
279 views
Looking for a cancer drug target database to guide sequencing of patient tumor DNA
I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s ...
12
votes
2answers
245 views
Why was it so hard to decode the corn genome?
My teachers growing up told me it was impossible to decode the maize genome. But yet its been done.
Why was decoding the genome so significant, and what made it so difficult?
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3answers
131 views
Alternate genetic codes in newly sequenced organisms
Variations of the standard genetic code are pretty rare, but as the cost of high-throughput genome sequencing continues to drop, there is a greater possibility of discovering additional exceptions. ...
