The process in which the DNA sequence of all or part of an organism's genome is obtained.

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Need to find software tools and relevant tutorial on data processing of the VCF format files from the whole genome tuberculosis bacteria analysis [closed]

Need to find the software tools and a relevant tutorials on data processing of the VCF format files generated during the whole genome tuberculosis bacteria analysis. Have found vcftools only. Please ...
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8 views

inter codon mutation statistical analysis

I am looking for an 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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20 views

Miseq loading with low concentration library

I have made a DNA library for miseq using truseq pcr-free dna HT kit (550bp insert). The problem is that at the end of library preparation and pooling, I need at least 2nM of library for denaturation. ...
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24 views

Superpatients for Cancer resistance

I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer. The article is ...
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1answer
87 views

Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?

My understanding is that PCR is carried out until a fluorescent nucleotide halts replication. The segments of DNA are fed through the capillary tube based on size, sifting through the segments from ...
4
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1answer
70 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 ...
4
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1answer
92 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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During bridge amplification of DNA sequences, why aren't sequences amplified in both orientations?

During bridge amplification, when sequences attached to adapters on the surface form "bridges" and are replicated, it seems like sequences with either end attached to the surface will be created. For ...
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1answer
28 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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344 views

Why was it so hard to decode the corn genome?

My teachers growing up told me it was impossible to decode the maize genome. But yet its been done. Why was decoding the genome so significant, and what made it so difficult?
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3answers
148 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 ...
0
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1answer
45 views

Simplest Biological Organism? [duplicate]

What is the simplest biological organism from which a DNA sample has been or could be obtained? Could the resulting DNA be processed and examined in such a way that the resulting information would ...
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5answers
1k views

How can I find a complete human genome file

I'm trying to figure out how I can download a file that represents the complete human DNA sequence. I don't care too much about the format – I'm able to write C++ code to parse it. FASTA seems like a ...
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24 views

What is the meaning of this poor sequencing result?

What is the meaning of this poor sequencing result? What is the problem? Can anyone guide me, please. Thank you.
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3answers
3k 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 ...
2
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1answer
27 views

Transcription rate expressed in microarray per hour

This article gives measurement of transcription rate and the unit they're using is microarray per hour. For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...
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2answers
46 views

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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1answer
249 views

What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...
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47 views

What good is the MinION?

This year, Oxford Nanopore MinION has been shipped to some researchers for testing. The advantage of a table-top sequencer for diagnostics and personalized medicine is obvious. Similarly, research ...
7
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2answers
180 views

What causes skewed lanes in a DNA gel electrophoresis experiment?

In gel electrophoresis, what causes effects like these (see collumn 11 in the first one, an collumn 6 in the second). ? (These images were samples that I took from an online activity we did for ...
2
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2answers
89 views

How do I perform recurring pattern mining or regular expressions of nucleotide sequences?

I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?
3
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1answer
62 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?
4
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2answers
328 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 ...
2
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2answers
96 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
66 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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2answers
59 views

In genome research, what is the problem in Mapping that may be caused by reads being too short?

In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back ...
5
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2answers
204 views

introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
3
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1answer
76 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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2answers
107 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 ...
7
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1answer
558 views

ChIP-seq vs ChIP-exo

I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites. As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
2
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34 views

coverage calculations approach for clipped reads [closed]

Experiment: deep sequencing for mutants in 700nt fragment. the fragment of dna was preamplified by primers flanking the fragment followed by hiseq. per base coverage was calculated by coverageBed -d ...
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condensed protocol for sequencing a portion of human DNA from buccal sample

Anyone have a short & sweet protocol for PCR amplifying a region of human DNA (chromosomal or mt, I don't care) extracted from a buccal sample: including validated primer sequences and preferred ...
2
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1answer
61 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 ...
7
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4answers
562 views

Looking for a DNA sequence

I am not a biologist. Please pardon me, if my question does not make sense. I am trying to obtain a DNA sequence for pattern analysis in Matlab. I used to generate random sequence ...
5
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2answers
2k 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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3answers
168 views

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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2answers
71 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 ...
4
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2answers
90 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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1answer
37 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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642 views

Finding proteins in DNA sequence

I have to do a task for a university task and I need to understand some things before figuring out how to do it. The task is the following: Find matches of known proteins (DNA-PolyI,II,III) to ...
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3answers
73 views

What is the datatype of dna sample?

What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?
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2answers
386 views

What are the limitations to current nucleotide sequencing technologies?

Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...
7
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1answer
65 views

How are whole Haplotypes for Sequencing isolated?

Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered ...
5
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3answers
179 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
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1answer
561 views

Number of reading frames in nucleotide sequence

In class of molecular biology was posed this question: "How many reading frames start in sequence of nucleotides 5' ... ATATGAATGATGACAT... 3' ?"
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what are hyperbranched amplicons in DNA sequencing?

I am reading an article about single-cell sequencing: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html And came across the concept of "hyperbranched amplicons". I googled for it but ...
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1answer
776 views

What is the difference between SNP and STR?

I thought that these were just different format of the same data. But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right? ...
3
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2answers
141 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 ...