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

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Interpretation of faint band for Linear Array HPV Genotyping Test

After having used the test for research it would appear as if it is very specific. What is one to make of bands that are there but faint? Or what if there are two bands and one is big and bold and the ...
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2answers
59 views

What is the frequency distribution of each base in a DNA sequence?

Can we say that the frequency distribution of each base in a DNA sequence is equiprobable? After the negative answer; i rephrase: Is there a use case in which the frequency distribution of the ...
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1answer
24 views

Genes that exist in old Affymetrix platform but not in the newer one

I am using two gene expression datasets from an Affy U95Av2 platform and an Affy U133 Plus 2.0 platform. When I map the Affy probe names to HUGO gene names, there are thousands of genes which exist in ...
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53 views

Online multiple sequence alignment with constraints

This is probably a naive question. I have accesssed the Clustal Omega online multiple sequence alignment tool at http://www.ebi.ac.uk/Tools/msa/clustalo/ for the first time, but I think I need to ...
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22 views

Paired-end illumina sequencing

I'm tying to understand the mechanism of paired end illumina sequencing, however I dont't understand why index primer 1 and index primer 2 are used. paired end illumina sequencing (YouTube). I ...
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35 views

How exactly are gaps defined in genomics?

My understanding is that when sequencing a genome, "gaps" refer to fragments which were not sequencing in the sequencer. Is this correctly? What are there other meanings to the term "gap"?
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41 views

How do high-throughput/NGS sequencers calculate quality scores?

I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the ...
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3answers
13k views

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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254 views

How can I preserve hair or saliva for future genome sequencing?

Suppose I want to preserve myself so that I can be reproduced as best as possible, in future or be simulated in future. At the moment full human genome sequencing is a bit expensive. One could get ...
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30 views

Which is the proportion of metagenomics reads that cannot be mapped in any genome?

I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable? I found a figure for viromics, which seems ...
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29 views

How to construct tumor phylogenetic tree?

I would like to know if anyone has tried any software that constructs tumor evolution trees where the trunks represent the common mutations and the private alterations are noted on each branch. I can ...
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84 views

Why do we encode information in DNA in binary and not in base 4?

I recently read an article about Harvard scientists encoding 700Tb of data in DNA strands. But they encoded the information in base 2, so T and G was a 1 and C and A was a 0. But why binary? Why ...
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50 views

Do plants have distinctive DNA genomes from each other like humans do?

Can exact same species of plant have a distinct genome from others of same exact species growing nearby or in a different place/country etc. ? Can a leaf be traced to the the exact plant based on DNA ...
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5k 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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334 views

In percentage, how much is the human genome (DNA) similar to the mouse genome?

Some guy argued with me against evolution theory, and he claimed that human and mice share 98% just like human and chimpanzee. I've tried to search online for a simple and accurate answer, but I ...
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49 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) ...
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53 views

how to compare Smith–Waterman algorithm implementations?

Assume that you have two softwares of smith waterman algorithm (with what ever heuristic they apply to speed up) for local sequence alignment of genomic sequences. I would like to know if for sure ...
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44 views

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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15 views

Trouble identifying a gene given an Expressed sequence tag

I have an assignment where we need to answer several questions about an EST, however, I'm having trouble getting started. My sequence contained a Not I site (clipped that) and no poly A signal. We ...
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28 views

Determine OTU identity using Blastn full database or organism specific database?

I am seeking opinions on the best way to determine OTU identity using Blastn. Would the best way to identify an OTU be to blast the OTU to the full nr/nt Nucleotide collection or to blast your OTU to ...
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37 views

Where can I find a file listing the genetic differences in humans?

I don't know much about genetics. For an arts project I'm looking for a human genome. I read that: Only about 0.1% of the genome is different among individuals, which equates to about 3 million ...
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2answers
112 views

What do Illumina HiSeq/MiSeq paired end reads look like?

My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this: R1: AAAAAACCCCCC R2: GGGGGGTTTTTT Where the ...
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115 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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28 views

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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43 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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23 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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50 views

Blood testing for chlamydia

I am working with the bacterium Chlamydia trachomatis. The main test for this species is the naat test, which is based on amplification. But I would like to know how the bacteria affects the blood ...
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25 views

Tool for translating chomosome, index numbers to sequence information

Is there a tool which allows me to transform information in the form (chromosome number, start index, end index) to sequence information? For example, something like (6, 43770819, 43770841) should ...
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71 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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26 views

Sodium hydroxide grade in library denaturation for NGS

If the NaOH, 1N which I bought does not have the label of molecular biology grade can it be used safely for library denaturation in NGS? Thank you!
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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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46 views

new DNA sequencing technologies? [closed]

Last year I did my thesis in the field of a new method for DNA analysis. Which I think is very interesting although I cannot seem to find any new methods in this field especially the SMRT sequencing ...
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21 views

Transgenic Plant-Gene source for introduction into host organism

Let's say the plant-gene itself is known, i.e. the exact neucleotide sequence is available in a gene bank (originally sequenced from a tree sample extracted RNA). Previous work has already successfuly ...
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50 views

Is there a good analogy that illustrates the difference between early DNA sequencing techniques and shotgun sequencing?

My first university biology classes begin in September. In preparation, but increasingly out of curiosity, I've been studying some basic biology. Saying that to say, I know as much about DNA ...
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47 views

How does a test like the Natera Panorama distinguish the child's genome from the mother?

Blood tests on an expectant mother, like the Natera Panorama, are now being used regularly to screen fetuses for chromosome abnormalities. At my wife's recent prenatal visit, she wasn't really even ...
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52 views

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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19 views

Can we take advantage of nanopore sequencing systematic errors to predict secondary structure motifs?

One of the methods of single-molecule sequencing, Nanopore sequencing, is based on traversal of DNA strand through a nanopore. Nucleotide is determined by measurement of ion current (when nucleotide ...
3
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1answer
34 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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58 views

Whole Genome Sequencing and B Chromosomes

Do whole genome sequencing techniques detect B chromosomes if such chromosomes are present? My understanding is as follows: How the DNA material in a B Chromosome is mapped depends on the reference ...
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1answer
57 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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16 views

How to identify genes in Ralstonia that synthesize PHB and promote granule formation?

The compound polyhydroxybutyrate (PHB) is of considerable industrial interest as a biodegradable substitute for plastic. PHB is synthesized from glycerol by the bacterium Ralstonia eutropha. PHB ...
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52 views

What is the result of modifying the reagents in the Sanger method?

If one of the dideoxynucleotides is omitted while using the Sanger method how would that affect the chain termination method of DNA sequencing?
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91 views

Standard practice for generating rarefaction curves from Next Generation Sequencing data

We have a few million 18S reads from a particular environment. The reads have been clustered into Operational Taxonomic Unit (OTU), and the OTUs annotated against a reference database. To generate a ...
4
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1answer
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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1answer
72 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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1answer
75 views

Does increasing the value of k in k-fold coverage requires more memory?

Study: Here is what is k-fold coverage which is know as sequence coverage. According to this, 2-fold coverage means the whole DNA is sequenced more twice in average. Question: If I have a genome ...
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1answer
90 views

How can I generate a random DNA sequence?

I've found this paper which involves the construction of 19-bp random DNA sequences, but I don't know enough biology to understand how this method works. Could someone explain it to someone who is ...
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2answers
145 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 ...
2
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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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32 views

why dna polymerase 3 requires a primer for replication [duplicate]

Why DNA polymerase 3 needs a primer to star replication.And whats happens when there is no AUG sequence on entire DNA.