Tagged Questions
0
votes
0answers
24 views
Reverse complement of reconstruction model for assembling reads
One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
6
votes
2answers
110 views
BLAST DNA Sequences Reversed
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:
It looks like it's ...
4
votes
3answers
89 views
Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?
I have a vector sequence and would like to find the following nucleotide sequence in it.
AASYWSRA
This query sequence uses several degenerate symbols, defined ...
8
votes
1answer
286 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 ...
11
votes
4answers
191 views
Why did high A+T content create problems for the Plasmoduim 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 ...
5
votes
2answers
129 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 ...
6
votes
3answers
189 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 ...
20
votes
4answers
760 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.
...
4
votes
3answers
94 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 ...
10
votes
3answers
386 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 ...
11
votes
1answer
280 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 ...
