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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138 views

Why do we use klenow fragment in pyrosequencing?

Why do we use klenow fragment in pyrosequencing instead of polymerase
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where i can download reference MSU7 rice genome?

I am working with RNA Seq data analysis. I have to download MSU7 rice genome. somehow i downloaded from "http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/...
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2k views

How to design internal primers?

I have sequences of the Cytochrome c oxidase I (COI) from several populations of Peringia ulvae (Mollusca; Gastropoda; Littorinimorpha; Hydrobiidae). I need additional COI sequences from a specific ...
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978 views

Whole Genome Sequencing vs Whole Exome Sequencing

I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:- I am looking at SNP's and ...
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42 views

What determines the amount of data you would get from a sequencing experiment?

When someone performs a sequencing experiment, what determines how much sequencing data you get from the machine (Illumina, PacBio, Nanopore, etc). Or maybe, put differently, how does the machine know ...
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168 views

Why are two forward and reverse priming sites depicted here? what do they do?

This question is in regard to the baculovirus expression system. (source: amsbio.com) Why do we need to generate primers for the polyhedrin promoter and the baculovirus? Primers are needed to ...
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453 views

dNTP concentration for reverse transcription from RNA to cDNA

Does it affect the results if I use the half of dNTP amount in a reaction that it says in my protocol? I usually use 4 microlitres per reaction and this time I did a mistake and I used 2. The final ...
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66 views

What factors should I consider when selecting a reference genome for mapping?

I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular ...
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186 views

Don't the radioactive labeled molecules of dNTPs or DNA harm themselves or their surroundings?

I'm reading some papers for the first generation sequencing methods and some earlier than them, like Ray's Wu first time DNA sequencing from a λ phage virus cohesive 5' ends. Ray Wu, like Maxam-...
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Ray wu DNA sequencing methodology understanding

I'm trying to understand the method which Ray Wu, developed to sequence the DNA 5' cohesive ends of a lamda phage. I'm reading these two papers written by him, but i stuck at the point where he uses ...
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2answers
120 views

Why do two different E. coli reference genomes have different lengths?

I've downloaded two different reference genome of E. coli (E. coli K-12 MG1655: U00096.1 and E. coli K-12 MG1655: U00096.2) and they have different lengths. I searched for the meaning of reference ...
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Does the string “…CATCAT…” appear in the DNA of Felis catus?

In Hofstadter's Gödel, Escher, Bach: An Eternal Golden Braid (GEB), the following claim appears: ...in the species Felis catus, deep probing has revealed that it is indeed possible to read the ...
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When is a DNA sequence a gene? [closed]

I am a newbie is DNA sequencing and BioInformatics. I am writing a school project that determines whether a DNA sequence is a gene or not using a Machine Learning Algorithm, Hidden Markov Model. After ...
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880 views

Collecting virgin fruit flies [closed]

Suppose that you place P generation wild type males and mutant virgin females in a vial and allow them to mate. You leave this vial undisturbed in the incubator for 12 days. Could you collect F1 flies ...
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2answers
88 views

Common mistakes when sequencing?

I've sequenced two genes of 15 dogs for SNP analysis. the chromatograms of one gene looked perfect but the ones of the second gene didn't look as good. To be precise, the chromatograms of one exon ...
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109 views

Find Mutations Frequencies by Cancer Type

Is there somewhere that has mutation frequencies by cancer type? So if I were looking at CML, AML, or even more generally at something like leukemia. Is there some database that would contain mutation ...
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139 views

Why is a screening process required in selection from a genomic DNA library?

After the process of construction we go for screening process of selecting a recombinant host. Which includes: DNA hybridisation Colony hybridisation Random primer labeling Nucleotide ...
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1answer
455 views

Two sets of chromosome and the sequencing output

Humans have two sets of chromosomes that are not connected in each cell. Am I correct? I assume while sequencing DNA both of these sets have to be sequenced and the output have to be provided in some ...
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DNA Sequencing and genotyping [closed]

Before going to the details of the question let me post a few other details- (I posted something similar and got no useful answers-probably because I didn't explain things properly or something else)- ...
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Sequencing two strands of dna

My background is not genetics. 2.I am not interested in knowing how dna sequencing or genotyping is done. 3. I am interested just in the nature of the results as described here. Now coming to the ...
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2answers
459 views

how does a dna probe work in DNA fingerprinting?

It says in my textbook ' after hybridisation with VNTR probe, the autoradiogram gives many bands of different sizes '. I tried looking on the net and it said there that probe is ' a radioactively ...
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71 views

C to T Transition Mechanism

I am seeing C to T transitions in my sequencing data, but also some strange signatures that follow along with that. I am trying to understand the biology of what is occurring. In the data I see more C ...
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1answer
142 views

Alignment of sequenced fragments in Next Generation sequencing (sequence assembly) [closed]

The NGS (Next Generation Sequencing) involves fragmenting the DNA to be sequenced. This is followed by attachment to beads or flow cells and then a localized PCR is conducted. Modified bases are added ...
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This Sequence Data (DNA) has very few Methionin-starts. How is that possible?

I'm working on my first sequencing related project and I'm trying to find proteins with a specific PFAM ID (PF11999). The project is called "MMETSP", I searched the annotations for that ID, identified ...
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2answers
175 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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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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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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105 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?
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How should “the human genome” be interpreted?

What does sequencing "the human genome" mean? Don't individuals have unique genomes?
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64 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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295 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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139 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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120 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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212 views

Does the cell have a mechanism to determine DNA sequence from protein?

Something like a reverse genetic code.
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1k 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 bases ...
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2answers
65 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
782 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).
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223 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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2answers
3k 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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278 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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156 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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518 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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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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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
166 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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327 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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1answer
102 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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1answer
75 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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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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559 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 ...