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.
20
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4answers
758 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.
...
15
votes
3answers
430 views
Is “computational biology” different from “bioinformatics”?
Are "computational biology" and "bioinformatics" simply different terms for the same thing or is there a real difference?
15
votes
3answers
138 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 ...
14
votes
2answers
171 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 ...
12
votes
1answer
2k 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 ...
11
votes
4answers
189 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 ...
11
votes
1answer
278 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
4answers
192 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.
10
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3answers
382 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 ...
10
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1answer
192 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 ...
9
votes
1answer
137 views
Is there a program that simulates biology on a molecular level?
Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
9
votes
3answers
251 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 ...
9
votes
2answers
191 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 ...
9
votes
1answer
118 views
Systems identification in small neural network
When analyzing data from cortex, we often try to understand what each neuron does in terms of its inputs from other neurons - a specific kind of a systems identification strategy. Most current ...
9
votes
2answers
141 views
Shortest strings not present in the human genome
What length are the shortest strings of DNA not present in any known person's genome, and what are they?
And is there a database online by which I could find this out?
9
votes
3answers
202 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 ...
9
votes
1answer
82 views
E. coli values for [enzymes], [metabolites] and kinetic rates
In my attempt to create a metabolic model of E. coli, I have found a comprehensive list of metabolic reactions and their stoichiometry. The one I am currently using is E. coli model iJO1366 (more ...
8
votes
5answers
191 views
Finding and Comparing Homologous Genes
I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal ...
8
votes
2answers
360 views
Databases for gene regulatory network graphs?
What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
8
votes
1answer
285 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 ...
8
votes
2answers
753 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 ...
7
votes
5answers
251 views
Introductory literature for synthetic / systems biology?
I'm a computer engineer (MsC Computer Engineering) who's looking to switch into the field of synthetic / systems biology.
I've got a comprehensive layman's understanding of evolution, genetics, ...
7
votes
2answers
148 views
How to compute properties of peptides ?
I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :
Length ...
7
votes
2answers
276 views
Use of amino-acid sequences versus use of nucleotide sequences in phylogenetic analysis
Reading a paper about gene evolution, I see that they do phylogenetic analysis for bacteria using protein sequences. They take the method from another paper.
I can suspect that amino-acid sequences ...
7
votes
1answer
233 views
How many gigabytes of DNA are there on earth?
The human genome is about 770 MB, the C. elegans genome is about 100 MB, the yeast S. cerevisiae is about 12 MB. Different other genomes have been sequenced: how many GB of genomic DNA we have now?
...
7
votes
5answers
197 views
Are there examples of encryption in nature?
There are examples of mathematics in nature such as Fibonacci number, fractals, etc. Are there examples of encrypted information?
What I am looking for is a pattern that seems random on the ...
7
votes
1answer
89 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 ...
7
votes
1answer
93 views
What role does a protein's size have on protein-protein interactions?
Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
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 ...
6
votes
2answers
100 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 ...
6
votes
1answer
161 views
Does DNA contain information beyond protein synthesis?
It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is ...
6
votes
3answers
187 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 ...
6
votes
2answers
219 views
Scoring sequence against position weight matrix
I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability
If I have a sequence say "AAPGTGASMHSGLLW" how would I score it ...
6
votes
1answer
124 views
What is Mendelian Randomization, and how is it used to infer causality in epidemiology?
Studies of human traits and diseases are inherently confined to observational studies, known as epidemiological studies. This can make it very hard to determine what actually causes a particular ...
6
votes
3answers
178 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 ...
6
votes
1answer
72 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 ...
6
votes
2answers
91 views
phylogenetic analysis of gene enrichment?
Are there any tools to do phylogenetic analysis of gene enrichment? This is, I have a list of genes from an experiment performed in several species, with a z-score that can be described as ...
6
votes
1answer
82 views
Has any large-scale origin-of-life simulation/experiment been done?
I have been thinking a little about the origins of life, and was further inspired by this question: How did the first self replicating organism come into existence?
I can accept that we don't quite ...
6
votes
2answers
86 views
How are Genetic Circuits Modelled?
I've read a recent Nature Methods paper by Moon T.S. et al, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure ...
6
votes
0answers
39 views
Using the IMGT/GENE-DB service to find RSS
I'm trying to get the data for the Human and Mouse 12 and 23 Recomination
Signal Sequences (RSS), to run a classification algorithm on it. I'm not a
biologist, so I apologise in advance for my ...
5
votes
3answers
367 views
How exactly are game theoretical evolutionary models described during implementation for computer simulations?
When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of "The ...
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 ...
5
votes
2answers
63 views
What is the state of automated quantitative analysis?
Quantitative analysis of microscope images is essential for many types of studies, but the techniques used most often are very labor-intensive. I have been able to find some literature about using ...
5
votes
1answer
145 views
How can I predict DNA binding affinities from a protein sequence?
Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?
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 ...
5
votes
1answer
1k views
Difference between strand-specific and not strand-specific RNA-seq data
I would like to ask the difference between strand-specific and not strand-specific dataset.
As far as I know, strand-specific data means that we know which strand the transcript is from.
I do not ...
5
votes
1answer
77 views
Assembly of metagenomic data
I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp).
I have tried multiple assemblers (CLC, ...
5
votes
1answer
185 views
Primer Dimer / Hairpin Algorithms
What are the algorithms / methods in use for the calculation of primer dimers and hairpins?
As an example, IDT's OligoAnalyzer tool will generate these analysis given particular sequences.
The ...
5
votes
1answer
84 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 ...
5
votes
1answer
118 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.
