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

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78 views

How to compare Smith–Waterman algorithm implementations?

Assume that you have two implementations of the 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 ...
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2answers
41 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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1answer
16 views

Is DNA sequencing coverage a function of sample purity?

How is coverage affected by the purity of a sample? And can coverage for a sample be affected by other things, like the library preparation or manner in which the sample was stored?
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1answer
19 views

DNA Sequencing Types & Qualities

I've been searching for a list of the types of DNA sequencing (e.g. Sanger, Next-Generation) and how prone they are to sequencing errors (None, Somewhat, Very), but I haven't been able to find ...
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7 views

mtDNA sequencing error rates

What is the method to estimate the error rate in mtDNA sequencing? E.g. we are given a profile like this: 16069T 16126C 73G 152C Is there a method, a table of known values, or any other way to say ...
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25 views

Distance between P5 and custom read 1 primer for Illumina HiSeq sequencing

I have a minigene library which is amplified with P5/P7 sites that looks like this [P7/barcode][constant region][ variable region ][18nt constant region][SP1][P5] (436nt total) We sequenced this ...
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1answer
368 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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1answer
41 views

Parameters of Variant calling analysis [closed]

What is the good or stringent parameter for variant calling. At present using the DP > 10 and Q > 30 for Variant calling. Is it ok.? Thanks
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1answer
30 views

what percent of DNA consider to be “junk”?

Does 98% of a whole human genome observe to be "junk" or 98% of each single human DNA observe to be "junk"or "non protein coding region"?
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1answer
61 views

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
52 views

How should “the human genome” be interpreted?

What does sequencing "the human genome" mean? Don't individuals have unique genomes?
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0answers
24 views

How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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1answer
73 views

What percentage of a Neanderthal's DNA could be in a Denisovan?

My questions arose from an online course video at 3:11-19 The professor mentioned that the Neanderthals were inbred with their cousins breeding together but the Denisovans were very diverse , with 70%...
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30 views

How do I know if the tRNA gene is under purifying selection from looking at a sequence dataset?

I'm having trouble figuring out how to tell if a tRNA gene is under purifying selection, just by looking at its sequence dataset. Such as this one:
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1answer
55 views

Perplexing by the way of estimating the shared or different genes between humans and chimps

We share 98.5% genes with chimps (it means we have 98.5% same DNA sequeces ),so there is about one percent difference .It means we can approximately differ from them by one base pair every hundred ...
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0answers
84 views

What is the another use of de Bruijn graphs in bioinformatics except DNA assembly? [closed]

I implemented own generic de Bruijn graph, which I use for DNA assembly (alphabet: A, C, G, T). I try to find purpose of de Bruijn graph for another bioinformatics problems, if some exists. I want use/...
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3answers
214 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 ...
0
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2answers
79 views

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

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 ...
0
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1answer
57 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 ...
0
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1answer
43 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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2answers
47 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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1answer
57 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
14k 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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1answer
37 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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38 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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1answer
98 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 didn'...
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2answers
68 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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2answers
6k 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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1answer
340 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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1answer
63 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) ...
3
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1answer
49 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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0answers
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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0answers
31 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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1answer
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
151 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 ...
3
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0answers
120 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?
3
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1answer
31 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 ...
3
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1answer
58 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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0answers
28 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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2answers
51 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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1answer
28 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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1answer
77 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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1answer
40 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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5answers
1k views

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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1answer
52 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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24 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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1answer
59 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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1answer
58 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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68 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 ...