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

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Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
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1answer
686 views

Digital Genomic Footprinting for ENCODE

I'm reading over the ENCODE Nature papers, and one of the papers referred to is "Global mapping of protein-DNA interactions in vivo by digital" by Hesselberth et al[1]. Genomic footprinting is a ...
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94 views

Cheapest Way to Measure Germ Density

I would like to measure the surface density of Staphylococcus bacteria and Rhinoviruses (only those two, to be specific) within my home. What's the cheapest way? The textbook procedure is to: rub ...
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1answer
58 views

Sequence of ribosomal RNA

Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli, ...
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1answer
177 views

Is there a detectable amount of bacterial DNA in the blood of infected persons?

With which bacterial infection in humans has it been shown that bacterial DNA can be found in the blood? If any is found it is likely not to be very much, and even difficult to distinguish from ...
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2answers
111 views

Sequencing from PCR

As far as I understand it, PCR can be used to make many copies of one gene. My question is, is it possible to sequence DNA after PCR and is it easier than sequencing it via other methods. If it is ...
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117 views

Is it possible to sequence only the 16S rRNA component? If so, how?

There have recently been several papers on using 16S rRNA as a way of identifying species (here, and here). I'm wondering if it's possible to sequence either just that subunit of the ribosome or just ...
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56 views

bam viewer that works on authenticated ftp urls with username/password combination? [closed]

Are there any BAM file viewers that will work on authenticated ftp urls with username/password combination? For example, something like this: ...
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4answers
407 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
522 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 ...
6
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2answers
187 views

Can I compare Shannon indices of metagenome gene data?

I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the ...
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136 views

Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping?

There are several companies (most notably 23andMe) providing SNP genotyping for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it ...
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336 views

What's the use of DNA sequencing results?

Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA "string" - the sequence of nucleotides. What's the use of that? It's just a "string" where nucleotides encode ...
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1k views

What exactly are computers used for in DNA sequencing?

I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing. There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts. ...
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2answers
322 views

Why are there N's after Sanger sequencing?

After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence. I know the N's mean that the computer can't tell what the base pair is, but why is ...
6
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1answer
95 views

Mechanics of going from DNA sequence to metabolic network

My apologies for possibly a naive question. I'm a statistics type and have been asked to assist with analysis of metabolic pathways (and networks). However, I would like to have at least a layman's ...
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161 views

protocol for pulldown of DNA breakpoints?

Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination ...
7
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1answer
721 views

How to clone and sequence a gene transcript of unknown sequence?

How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA ...
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3answers
101 views

How to create a collection of anonymous sequences for teaching and testing? [closed]

I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection. The sequence files would be used for teaching and for testing ...
12
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3answers
678 views

Why do restriction enzymes tend to have an even number of bases in their recognition site?

When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases. I wondered if this was just a co-incidence, so I took the data from this ...
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4answers
396 views

Questions to ask to a panel of people that will be sequenced

Some genes have been shown to be associated with left-handedness. Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are "right or ...
12
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1answer
536 views

Sequencing the genomes of polyploid organisms

I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about ...
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2answers
299 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 ...
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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 ...
12
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1answer
344 views

Looking for a cancer drug target database to guide sequencing of patient tumor DNA

I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s ...
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2answers
272 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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160 views

Alternate genetic codes in newly sequenced organisms

Variations of the standard genetic code are pretty rare, but as the cost of high-throughput genome sequencing continues to drop, there is a greater possibility of discovering additional exceptions. ...