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.
4
votes
1answer
40 views
Parse PDB using DSR-PDB Library
I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose.
I've encountered a problem. This library interprets CD1 atom of ILE ...
6
votes
2answers
87 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
2answers
221 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 ...
3
votes
0answers
62 views
Organize sequence database [closed]
I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be ...
4
votes
1answer
87 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 ...
7
votes
2answers
282 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 ...
2
votes
1answer
68 views
How to build S16 rRNAs phylogenetic trees?
Here is what I know so far:
Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones.
There are stem regions in the ...
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 ...
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 ...
4
votes
1answer
120 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 ...
2
votes
2answers
60 views
Microbiome Data
How is it possible to access microbiome data like that found here? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the Human Biome Project. Thanks for any ...
5
votes
3answers
368 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 ...
2
votes
1answer
110 views
How to learn DNA Origami
Can you tell me is there any good softwares and tutorials which can be used to learn DNA Origami. I am new to this and want to learn from basics.
Advance thanks for your help
edited: INSILICO
9
votes
1answer
83 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 ...
4
votes
1answer
60 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 ...
15
votes
3answers
435 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?
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 ...
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, ...
9
votes
1answer
138 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
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?
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
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, ...
3
votes
2answers
118 views
JMol “calculate HBONDS”: which atom is the donor/acceptor?
JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds.
Here's one line from an example ...
5
votes
1answer
191 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 ...
4
votes
1answer
49 views
Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology
Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?
I have tried the following:
...
1
vote
1answer
28 views
Where can I find a transcriptome of a normal uveal melanocyte?
I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?
1
vote
1answer
51 views
TFBS predictions for yeast and pombe?
Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
7
votes
5answers
252 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, ...
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 ...
2
votes
0answers
111 views
Too few transcripts from transcriptome assembler Oases
I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.
Here is my running command:
...
4
votes
0answers
77 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 ...
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?
6
votes
2answers
92 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 ...
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 ...
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?
...
8
votes
2answers
369 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 ...
3
votes
1answer
100 views
Epilepsy explained by computational neuroscience
A few years ago, on my maths masters, I did a module in theoretical neuroscience. I was shown that the mathematical framework the course developed for neurons, with a small adjustment in the ...
4
votes
1answer
47 views
How to find ion/water channel related genes
We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the ...
4
votes
1answer
46 views
What value type would a chromosome position be in a database or form?
I wanted to create a tool for some fields like SIFT, Phenotype, etc..so for example I know Phenotype will have "Text" values or SIFT will have some determined values from a drop down list...but what ...
8
votes
5answers
195 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 ...
1
vote
0answers
48 views
SAM and Reverse Complements [closed]
Assume a read aligner (such as e.g. BWA) is fed with a pattern P = GACT. Now, the text that ...
2
votes
0answers
143 views
Turn off multithreading in pymol [closed]
By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core?
Motivation:
I have a large collection ...
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
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 ...
1
vote
1answer
69 views
Generating custom human DNA sequences based on traits such as eye colour?
I'm wondering if it would be possible to create software (unless some already exists, but I couldn't find any) to generate human DNA (the base pairs on the double helix) containing genes representing ...
2
votes
2answers
66 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
254 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
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.
...
