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 ...

learn more… | top users | synonyms (1)

8
votes
1answer
206 views

Mass spectrometry versus western blotting for validation

I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In ...
8
votes
1answer
126 views

What sample sizes are ideal for carrying out Bayesian Skyline Plots?

I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 ...
8
votes
1answer
376 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 ...
8
votes
1answer
146 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 ...
8
votes
0answers
96 views

Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
7
votes
5answers
389 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
424 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
217 views

What is the difference between sequence, reads, and contigs of genetic material?

Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example? I am new to bioinformatics, and I have not found any conclusive ...
7
votes
5answers
418 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
2answers
226 views

RNA-Seq library construction challenges: the biases of RNA fragmentation vs cDNA fragmentation

I recently watched a presentation on RNA-seq that covered some of the choices one can make along the way, and I didn't fully understand one of the choices in particular. Near the beginning of the ...
7
votes
4answers
552 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 ...
7
votes
1answer
136 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
89 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
7
votes
0answers
112 views

At which step apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

I am trying to understand what is the best practice when preprocessing microarray data using a detection filter (on scanner p-value). Suppose I have a microarray dataset that I have to normalize with ...
6
votes
3answers
824 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
415 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
719 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
1answer
90 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
287 views

introduction to Chip Seq

I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've ...
6
votes
3answers
149 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 ...
6
votes
2answers
129 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
3answers
324 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
2answers
120 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
240 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
1answer
47 views

What is a positive epitope fragment

What is a positive epitope fragment? I found one paper on the subject: COBEpro: a novel system for predicting continuous B-cell epitopes by Michael J. Sweredoski and Pierre Baldi
6
votes
2answers
108 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
1answer
459 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?
6
votes
1answer
39 views

Comparison of gene expression time series in vitro and in vivo

I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days ...
6
votes
1answer
226 views

Find protein homologs with BLASTp

I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases. I'm using evalue of 0.00001 as threshold. I would like to filter queries having hits with >90% ...
6
votes
1answer
220 views

How can promoter binding sites be determined?

I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it ...
6
votes
1answer
105 views

Book suggestion on computational molecular evolution

I'm currently reading Computational Molecular Evolution by Yang. Can you recommend alternative books? I am finding it to be lacking on conceptual discussion (it's more focussed on the mathematics and ...
6
votes
1answer
290 views

Models of quorum sensing for multi-agent systems

Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model ...
6
votes
3answers
974 views

What percentage of protein isoforms have different functions?

I am looking for studies on how many protein isoforms have different functions, preferably in human. We know that a great many, if not most, of human genes are alternatively spliced and that many ...
5
votes
3answers
222 views

Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
5
votes
2answers
205 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
109 views

The meaning of RNA-seq data

many papers I read mentioned "RNA-seq data". While searching for the meaning of this word, I could not find any layman's definition. As far as I understand, RNA-seq data is the complete RNA ...
5
votes
3answers
199 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
5
votes
3answers
138 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
5
votes
2answers
94 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
2answers
57 views

What ways are there to determine how big genera are?

I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data ...
5
votes
1answer
130 views

Sequence evolution simulation tool

I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate ...
5
votes
5answers
165 views

What are some examples of evolving networks in biology?

I'm a master student working on networks analysis in general. A network is something that has nodes and there are links between the nodes. Nodes and links could have attributes. An evolving network is ...
5
votes
1answer
200 views

Definitions and examples of some math-releated ecology branches

I would like to have an example of application and a brief description/definition (two or three lines) of the following fields. I would like to understand the exact differences between them. Other ...
5
votes
2answers
258 views

How to get smallest subtree containing a set of nodes from BioPhylo?

I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and ...
5
votes
1answer
284 views

Which way to run BLAST?

I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways: Create a BLAST database of the ...
5
votes
1answer
108 views

Determining if a Protein Model Contains a Backbone Clash

I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be ...
5
votes
1answer
89 views

Base Substitution Probabilities Derivation

In Felsenstein's 1981 Paper Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, he describes (in equations (6) and (7)) a derivation of the equation of the probability of a ...
5
votes
3answers
404 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 ...
5
votes
1answer
540 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
116 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 ...