Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ...

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26
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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. ...
18
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3answers
1k 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?
17
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3answers
189 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 ...
13
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2answers
273 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
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4answers
430 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 ...
12
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3answers
689 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 ...
12
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1answer
6k 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 ...
12
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1answer
354 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 ...
11
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4answers
254 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.
11
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3answers
523 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 ...
10
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2answers
197 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?
10
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1answer
504 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
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5answers
608 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 ...
9
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3answers
385 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
3answers
107 views

Standard letter for 5-methylcytosine

I'm working on a piece of software that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base. At the moment, the bases ...
9
votes
2answers
305 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
150 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
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2answers
807 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 ...
9
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2answers
127 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, ...
9
votes
1answer
114 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 ...
9
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1answer
141 views

Protein data bank syntax: Can two protein secondary structures “overlap”?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
8
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1answer
164 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?
8
votes
2answers
675 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 ...
8
votes
2answers
2k 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 ...
8
votes
1answer
418 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? ...
8
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2answers
509 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 ...
8
votes
1answer
278 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 ...
8
votes
1answer
713 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
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2answers
974 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 ...
8
votes
1answer
237 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.
8
votes
1answer
56 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 ...
8
votes
1answer
128 views

Is there a comprehensive database of fossils (with images) online?

Not sure if this is the best stackexchange to ask... I have not been able to find a decent database of fossils on the web, does one exist? Here are some of the links I have found through Wikipedia ...
7
votes
5answers
314 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
273 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
3answers
127 views

What is the potential function of ultra-conserved elements in the genome?

If selection pressure results in conservation of DNA sequences, what is the most plausible explanation for the existence of ultra-conserved elements (refs here and here) given that there hasn't been ...
7
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5answers
311 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
124 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
4k 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 ...
7
votes
1answer
165 views

List of np-hard problems in biology/bioinformatics

I'm not sure if this is the right place for this but... I am looking for a list of computationally "hard" problems such that if a problem from this list could be solved effectively, it would be ...
7
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0answers
71 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 ...
6
votes
3answers
633 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 ...
6
votes
3answers
340 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
1answer
85 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
110 views

Examples of references for mathematical approaches in bioinformatics that are applicable to linguistics?

Do you have any classic references for mathematical approaches in bioinformatics that are applicable to linguistics (or vice versa)? EDIT I am mainly interested in approaches to reconstruct the ...
6
votes
1answer
354 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
264 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
4answers
366 views

Suitable introductory book on Bioinformatics for a computer scientist?

Do you have any suggestions on a suitable introductory text on bioinformatics for a computer scientist? Any recommendations with pros and cons of different books would be appreciated. I'm mainly ...
6
votes
2answers
109 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
2answers
189 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
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1answer
258 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 ...