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

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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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748 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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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 ...
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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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84 views

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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124 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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188 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 their ...
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82 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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148 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 ...
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36 views

Determining the Accuracy of DNA Testing

The DNA Testing firm in the below article claims that its tests were "99.99 per cent" accurate. http://www.telegraph.co.uk/news/uknews/1322077/False-DNA-test-led-father-to-reject-daughter.html ...
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125 views

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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311 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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136 views

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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73 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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51 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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678 views

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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6k 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 ...
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803 views

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 ...
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202 views

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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45 views

constitution of read and gene region (IGV)

I work with fastq files containing NGS reads for some human DNA regions. The reference genome is hg19. I had two fastq files (pair-ended). I generated alignment BAM files. I used "bwa" and samtools to ...
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35 views

Is there any websites that provide the DNA sequences of food samples?

We can get many DNA sequences at NCBI websites for free. Is there any websites that provide the DNA sequences of food especially meat, for free? When I read papers regarding food authentication, ...
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73 views

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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69 views

Why are sequencing reads shorter than PCR products?

I have desinged and tested primers for RT-PCR, then purified the PCR products from the gels and send them to sequence at GATC (SUPREMERUN) using the forward primers. After blasting the reads to ...
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1answer
73 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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36 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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143 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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Are there any major noticeable limitations to genome sequence compression methods that use reference templates?

Recently, I have been researching about big data analytics in biochemistry, and started wondering about how genome sequence compression could affect analysis. Of all the method listed on the ...
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Gemini usage of --sample-filter

I am using gemini to query databases made from vcf files, which contain data from multiple samples. However, I need to query data only from one sample, (for which I currently use grep to filter the ...
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37 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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84 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, ...
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241 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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187 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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2k 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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117 views

Whole gene sequence analysis to determine source infection [closed]

Is it possible to use whole gene sequence analysis to distinguish between a common source infection and a person-person disease transmission?
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26 views

Do eukaryotes assimilate DNA that is floating in the extracellular membrane?

Prokayotes, which replicate primarily using binary fission, don't get much genetic diversity. For this reason, they take in any genetic material they encounter, in a gambit to help them better adapt ...
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RAD sequencing: choosing the appropriate enzyme?

I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC ...
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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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24 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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127 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 ...
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1answer
102 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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299 views

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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1answer
48 views

In DNA sequencing, is “mate pairs” synonymous with “paired ends”? If not, how do they differ?

By just looking at Roach et al's paper I get the impression that they are the same thing, and the Wikipedia URL for the former is a redirect to the latter. However, I suspect they are not exactly the ...
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161 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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169 views

In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis. I also understand cloning can be a ...
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3answers
157 views

What is the difference between sequence alignment and sequence assembly?

I read the wikipedia page about sequence alignment and sequence assembly but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence ...
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2answers
136 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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1answer
74 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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1answer
50 views

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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1answer
2k 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
54 views

Questions on adding a protein to a DNA library [closed]

Two questions regarding finding the DNA sequence of a amino acid sequence (AA): 1) If you are able to find out the mRNA sequence of an AA, then don't you automatically know the DNA sequence? 2) ...