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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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Is DNase treatment necessary before RNA sequencing?

Is it necessary to treat total RNA with DNase before sequencing it? In particular, if the library prep relies on a poly-A enrichment, is it necessary to remove DNA, knowing that genomic DNA does not ...
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1answer
56 views

Is my Y-chromosome the same at 78 as it was at 18?

How accurate is a Y-dna test at age 78?
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44 views

Question about phylogenies and DNA sequencing

I'm reading this web page which talks about phylogenies and DNA sequencing: https://bioinf.comav.upv.es/courses/biotech3/theory/phylogeny.html A certain sentence says, "If we consider dolphins and ...
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43 views

How do you sequence a tree genome? [closed]

I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a ...
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DNA Longevity in Keratin, Ivory and other Bioplastics

For how long is DNA viable for extraction and/or sequencing in bioplastics created by the human body? I checked out a few links online, and this article gives a record of about 7000 years for frozen ...
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Can PCR duplicates have complementary sequences?

It is common when analyzing paired-end whole-genome shotgun sequencing data to check for and eliminate PCR duplicates. The reasoning is that the probability of sampling a fragment of the genome of the ...
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1answer
903 views

How is DNA testing used to differentiate between different species?

How is DNA testing used to determine that specimens belong to different species, rather than being subspecies, or members of the same species? Usually the definition of species is about the ability to ...
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1answer
324 views

Limitations of Gibson Assembly method

Why is the Gibson assembly method limited to ~8 fragments and what can be done to raise this limit? Why is the method called "seamless" and what are the advantages compared to annealing ...
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121 views

Repeating sequences of genomes

How can we estimate what portion of a genome is repeating sequences without sequencing it? Thank you
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530 views

PCR products with no band in gel

I am a PhD student and stuck with the no band in the gel results. I am using the following 1 microliter Primer R (20mM) 1 microliter Primer f (20mM) 1 microliter dNTP (10mM) 1 microliter DNA ...
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DNA as a digital storage medium; sequences algorithmically avoided for safety reasons (or should be)?

Safety for the environment is probably implicit here as well, but the focus should be on the people who may come in contact with large amounts of synthetic DNA used to encode information as a data ...
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46 views

Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
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64 views

What does it exactly mean to sequence the genome of a species?

Since all organisms are different from each other - that is, we all have different alleles, some SNP, microsatellites, etc. -, what does it exactly mean, for the genome of a species, to be sequenced? ...
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What are the exact reason causing missing calls in a VCF file from exome sequencing?

My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is ...
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1answer
201 views

What is the difference between contig- and read-based sequence alignment?

I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused ...
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2answers
256 views

Is it possible to obtain single strands of DNA in solution? [closed]

Being that it is relatively simple to extract DNA from a variety of sources, what further technique can be used to separate the two complementary strands in solution?
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1answer
81 views

How does a polymerized TruSeq adapter affect sequencing reads?

I am trying to build a NGS library on enriched DNA (DNA length = 93 bp). I am using PCR amplification with two overhanging primers, both containing Illumina adapter sequences (Universal Adapter & ...
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187 views

What are the effects of buffer on genomic DNA shearing by sonication?

Expt: I have isolated genomic DNA from LNCaP cells and would like to crosslink a small molecule (Chem-seq) to the DNA. The small molecule is an alkylator so it will crosslink DNA on its own. The ...
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1answer
80 views

What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci?

The article about "rapture sequencing" found here says: "This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses ...
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1answer
311 views

Quantifying DNA in a band on gel electrophoresis

I am a first year science undergraduate and I am just asking this as a more theoretical question rather than for carrying out a protocol, so I would appreciate if answers do not involve lots of ...
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2answers
459 views

What are the pros & cons of site-directed mutagenesis? What are the alternatives?

For a lab course we have been assigned to "remove a stop codon, using mutagenesis, that is in the middle of a gene in order for the full gene to be expressed. This will then fluoresce." To do this we ...
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77 views

How can DNA profiling be used to determine the number of organisms from a specific species that is within a certain area?

Here is the tedious exam question that asks this: question 8(b). https://drive.google.com/drive/folders/0B23NLD5L6099VWJya3dfLVJpbmc The question states: In 2007, the brown bear was a threatened ...
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1answer
157 views

16s rRNA Sequencing From Gut Microbiome (stool)

Do I extract RNA or DNA from gut microbiome (stool samples) if want to do 16s rRNA sequencing?
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1answer
96 views

How do we know which Eulerian path corresponds to the DNA sequence?

Bioinformatics textbooks explain one method to reconstruct the whole DNA sequence from multiple reads. The method builds a graph and finds a Eulerian path in it. The Eulerian path corresponds to a DNA ...
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2answers
255 views

What does chrUn mean in the output from a Bowtie run on human sequences?

After having performed an alignment using bowtie2 and GRCh38 as a reference sequence, I got inusual matches on chrUn. Here a small part of the SAM file: ...
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1answer
6k views

Why is only one primer used for DNA sequencing instead of two?

I understand that PCR uses two primers that anneal to the two ssDNA's in order to exponentially amplify a DNA and that Sanger sequencing uses only one primer because a sequence can be determined with ...
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2answers
92 views

Finding protein motifs by running sequence analysis in protein BLAST

I've run the following sequence (bottom of page) in NCBI protein BLAST and its been identified as Zn-dependent alcohol dehydrogenase. Next I want to see what protein motifs are in this protein. Where ...
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2answers
193 views

Actual determination of the DNA sequence in the shotgun approach?

I'm studying bioinformatics and I'm confused by shotgun sequencing. In Sanger sequencing we break up the DNA and use ddNTPs in order to determine the exact position of each neucleotide. How exactly ...
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1answer
58 views

How to find sequencing data of a specific drosophila strain

I'm trying to correct low coverage parts of an assembly of these PacBio reads with Illumina data. According to PacBio they "have sequenced adult males from a subline of the ISO1 (y; cn, bw, sp) strain ...
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56 views

An efficient and free method of assembling a large number of Sanger sequencing reads?

I have a rather large number of Sanger Sequencing reads.  Is there a automated method in either Ugene or a similiar freeware that allows you to quickly assemble forward and reverse reads. Ideally ...
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371 views

Where can I get my exomes sequenced?

I am a private individual and I want my exomes sequenced, I don't know of any place that will keep my data confidential as I read reports of companies sharing this data with insurance companies. I ...
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1answer
4k views

Are SNPs and alleles the same thing?

It seems to be quite difficult to find an answer to this. Are SNPs the same thing as alleles?
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163 views

Can DNA sequencing of food provide quantitatively the fraction of protein from chicken vs soy?

There is some news about a report from Canada's CBC about fast-food chicken items containing as much as 50% soy protein, based on DNA testing. I won't do the report the service of linking to it ...
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142 views

VCF files - examples for haploid organisms

I am trying to self-learn some aspects of bioinformatics (coming from a stats background), and i am trying to find / download some VCF files for haploid organisms as an input to some statistical ...
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How to design a ChIP-exo experiment with controls?

Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment? Is it even necessary to run a control (similar to input DNA for ChIP-seq)? I'm looking for any references ...
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Why do we use klenow fragment in pyrosequencing?

Why do we use klenow fragment in pyrosequencing instead of polymerase
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1answer
63 views

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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963 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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41 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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163 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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428 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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55 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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1answer
179 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
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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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4answers
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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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2answers
90 views

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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788 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
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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 ...