The process in which the DNA sequence of all or part of an organism's genome is obtained.

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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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30 views

DNA densities in different sources of the human body [closed]

I'm interested to know if there is any research in the density of DNA in different sources of the human body. By DNA density I mean the number of bonded between the nucleotides per mass or volume of ...
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65 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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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 ...
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24 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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340 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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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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33 views

Artificial Gene Alteration [closed]

Is artificial alteration/"correction" of genes conceivable? I know viruses can manipulate DNA or RNA to replicate itself, but its only temporary, right? If this were possible, how would it be gone ...
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43 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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22 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.
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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 ...
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27 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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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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185 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 ...
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45 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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2answers
163 views

What causes skewed lanes in a DNA gel electrophoresis experiment?

In gel electrophoresis, what causes effects like these (see collumn 11 in the first one, an collumn 6 in the second). ? (These images were samples that I took from an online activity we did for ...
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2answers
86 views

How do I perform recurring pattern mining or regular expressions of nucleotide sequences?

I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?
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61 views

How did the Human Genome Project Sequence DNA [closed]

There are quite a few methods of sequencing DNA. What method was used (or used most often) to sequence the human genome in the Human Genome Project?
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59 views

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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2answers
303 views

Why is assembling paired end illumina without any input parameters an important problem?

In one of the comments in this question about multiple sequence alignment, it was stated @5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any ...
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2answers
91 views

chimeric sequences [closed]

I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. ...
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27 views

What percentage of chimeric takes up in a cDNA library? [on hold]

I get a cDNA library of species of Mollusca,and complete some of the clones with polyA tails.But when I translate them with three frames,I find there is a large percentage of sequences that cannot ...
2
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1answer
61 views

How was Restriction Site of EcoRI sequenced?

The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977) How was the restriction site of EcoRI sequenced ?
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In genome research, what is the problem in Mapping that may be caused by reads being too short?

In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back ...
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190 views

introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
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1answer
74 views

What is meant by single molecule sequencing?

When sequencing papers refer to single molecule sequencing, what is their definition of a "molecule". Are they saying base by base? The entire DNA chain in a chromosome can also be though of as a ...
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How were the first primers made

I keep reading about how primers are useful in pcr -- they allow you to select a specific dna region. Similarly, in NGS or Sanger sequencing they give you a starting point. The primers I see are about ...
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548 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 ...
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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 ...
2
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1answer
60 views

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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559 views

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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2answers
2k views

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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161 views

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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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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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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1answer
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What is mRNA expression level?

I cannot find clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference. Thanks!
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611 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 ...
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3answers
70 views

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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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 ...
7
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65 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 ...
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178 views

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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538 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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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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673 views

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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139 views

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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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 ...