Bioinformatics is a broad field that interfaces a variety of life science disciplines with a variety of quantitative sciences. Questions on Bioinformatics are expected to have a direct biological component to them or they may belong on Stackoverflow or Superuser.
2
votes
2answers
68 views
Consensus codon optimization by organism
Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables ...
4
votes
2answers
57 views
Main methods used to predict functional annotations in GO
Can someone provide me some information about the main method used to predict the inferred electronic annotations in Gene Ontology?
9
votes
3answers
269 views
Source of DNA sequences
I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case ...
6
votes
3answers
197 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 ...
21
votes
4answers
774 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.
...
12
votes
1answer
3k views
What is the significance and method behind Ramachandran plots?
My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and ...
5
votes
2answers
133 views
First pass protein structure prediction
I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I ...
6
votes
3answers
179 views
Compressing structural information in PDB files
There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
5
votes
1answer
86 views
How do I prepare a PDB for submission to the Protein Data Bank?
I have a couple structures that are nearly ready to be deposited in the PDB. Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked ...
9
votes
2answers
200 views
How can I pare down a PDB file in Python to only include specific residues?
I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session ...
6
votes
1answer
73 views
Is there a tool to find the action of an enzyme in a metabolic pathway?
Is there any tool to search the biochemical action of a particular enzyme in a metabolic pathway of an organism? In other words, how can I find if enzyme "E" is involved in the metabolic pathway for ...
3
votes
1answer
256 views
Displaying nucleotide at a single position from RNA-seq reads in a BAM file
How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am ...
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 ...
5
votes
1answer
124 views
Is it possible to add a new sequence to a blast database without recreating it from scratch?
I have a new sequence and I want to add it to a pre-constructed BLAST database containing other sequences. The makeblastdb help does not give any hint on this regard.
10
votes
4answers
198 views
What can you tell about a person, having only their whole genome as information?
Well, the question is in the title, no explanation need.
7
votes
1answer
90 views
PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?
I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
10
votes
3answers
393 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 ...
7
votes
1answer
34 views
Downloadable worldwide database of disease statistics?
I am looking for a downloadable database of disease statistics. I have emailed the good folks over at HealthMap, but they haven't gotten back to me yet.
As far as I can tell, their data relevant to ...
11
votes
1answer
284 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 ...
10
votes
1answer
220 views
How do I get the current “camera position” in PyMol so I can reuse it in scripts?
I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same ...
14
votes
2answers
180 views
When does BLAST fail to align 2 DNA sequences?
This is an assignment that had confused me for a long time. So I think you guys who study computational biology might be interested. The original question is:
Find the two most similar DNA ...
8
votes
2answers
771 views
How can rooted and unrooted (phylogenetic) trees be distinguished from one another
I understand that both are similar in structure
But how can they be easily identified as one or the other?
Is it simply based on the presence or lack of a named root (the root is identified as a ...
16
votes
3answers
141 views
What is the optimal frame size for protein secondary structure prediction methods?
The whole question is
What is the optimal frame size for the second and third generation protein secondary structure prediction methods? Justify your answer.
I remember it has something to do ...
9
votes
3answers
219 views
Human disease and associated phenotype database?
Does anyone know of any good databases that contain symptoms for diseases and other ailments in humans? I've tried working with UMLS, but thats been impossible to work with. I've also tried working ...
