Questions tagged [dna-sequencing]

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

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62 views

coverage calculations approach for clipped reads [closed]

Experiment: deep sequencing for mutants in 700nt fragment. the fragment of dna was preamplified by primers flanking the fragment followed by hiseq. per base coverage was calculated by coverageBed -d -...
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condensed protocol for sequencing a portion of human DNA from buccal sample

Anyone have a short & sweet protocol for PCR amplifying a region of human DNA (chromosomal or mt, I don't care) extracted from a buccal sample: including validated primer sequences and preferred ...
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Do you have experience with PacBio?

I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have ...
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Looking for a DNA sequence

I am not a biologist. Please pardon me, if my question does not make sense. I am trying to obtain a DNA sequence for pattern analysis in Matlab. I used to generate random sequence ...
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What causes skewed lanes in a DNA gel electrophoresis experiment?

In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)? (These images were samples that I took from an online activity we did for class)...
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How do we know that everybody's DNA fingerprint is unique?

How do we know that everybody's DNA fingerprint is unique? I know, I know, everybody's DNA is unique. But when we do DNA fingerprinting, we're looking at very specific regions of high variability. ...
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Detecting cancer or a genetic predisposition based on DNA sequencing

I am not by any means a biologist - so go easy. What would be a method for determining whether or not a patient has cancer based only on a genomic sequence? Update Thanks for the help in revising ...
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Is there a database containing sequences of human cell lines?

I'm looking for the whole genome sequences of several human cell lines, e.g., A549 or Ea.hy.926. Is there a database specifically dedicated to human cell lines?
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Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...
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What is mRNA expression level?

I cannot find a clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference.
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What is the datatype of dna sample?

What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?
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How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
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Why do we need deep sequencing?

Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological ...
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what are hyperbranched amplicons in DNA sequencing?

I am reading an article about single-cell sequencing: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html And came across the concept of "hyperbranched amplicons". I googled for it but ...
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What is the difference between SNP and STR?

I thought that these were just different format of the same data. But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right? ...
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What to do with a DNA sequencer? [closed]

My school is very fortunate to have a DNA sequencer, and I want to find an opportunity to learn how to use it. I'm currently taking AP Biology this year, and I hope to do an independent study in ...
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Basic text/notes on DNA structure (for non-biologists)

I am a mathematics grad student researching knot theory, and I've recently discovered that there is a connection between knot theory and DNA structure (if I understand correctly, when DNA strands ...
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Why only heterogeneous SNVs for validation using genotyping arrays?

I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called ...
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How to calculate extent of Sequence similarity [closed]

I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity. I have a Problem Statement: we have a sensor (...
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What species have had their genomes sequenced/are being sequenced?

The human genome project released it's first complete genome nearly ten years ago. Since then many species have also been sequenced. I am trying to find a list of completed (and possibly ongoing/...
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Is it possible to clone a Neanderthal?

As Neanderthal DNA has been sequenced, is it possible to create a living Neanderthal?
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DNA preparation for sequencing

In shotgun sequencing method or some related method that DNA is break up into random fragment. The fragment that have about 3kb in size is inserted into plasmid by enzyme ligase and then plasmid ...
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Why can't we observe haplotypes directly?

I am completely a noob to biology and DNAs, but recently I am looking into EM-algorithm used in the case of re-constructing haplotypes from genotype data. I am just wondering what exactly in the ...
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Any tool to align whole genome sequence data to another genome and give exon regions a higher mark?

I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I ...
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Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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Are there beneficial genetic mutations identified by consumer DNA genotyping?

I'm looking at services like 23andme, and see that they identify a wide variety of genetic-based risks, like predisposition to diseases, hair loss, cancer, etc. Are there a more "positive" DNA ...
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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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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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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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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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What's the difference between shotgun sequencing and clone based sequencing?

In a lecture during my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera ...
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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 ...
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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 their ...
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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 well....
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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 as:...
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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 ...
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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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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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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 ...
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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 the ...
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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 ...
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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 (...
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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 ...
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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, ...
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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 ...
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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 ...
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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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Why did high A+T content create problems for the Plasmodium 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 ...
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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 ...
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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 ...