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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6
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1answer
218 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 ...
11
votes
4answers
236 views
3
votes
1answer
50 views

Is copy number variation dynamic?

Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...
1
vote
1answer
91 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
5
votes
2answers
73 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 ...
3
votes
2answers
223 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 ...
3
votes
1answer
109 views

Can compounds be predicted from Polyketide synthases gene clusters?

I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this ...
17
votes
3answers
178 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 ...
2
votes
1answer
111 views

How can I compare rates of evolution for two sets of proteins?

I have a list of candidate proteins as the result of my analysis. I am now trying to find various characteristics that they have in common. One of the things I would like to check is if my candidates ...
6
votes
2answers
102 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 ...
4
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1answer
54 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 ...
9
votes
5answers
533 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
1answer
159 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?
5
votes
1answer
104 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 ...
13
votes
2answers
237 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 ...
4
votes
0answers
80 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 ...
8
votes
2answers
1k 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 ...
5
votes
1answer
158 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 ...
3
votes
2answers
68 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 ...
2
votes
1answer
77 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 ...
7
votes
1answer
259 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
591 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 ...
2
votes
1answer
166 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
4
votes
1answer
80 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 ...
4
votes
1answer
50 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
92 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, ...
6
votes
2answers
181 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 ...
10
votes
2answers
180 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
234 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 ...
5
votes
1answer
350 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
80 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: ...
2
votes
0answers
209 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 ...
4
votes
1answer
122 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 ...
1
vote
1answer
33 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
65 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 ...
6
votes
2answers
107 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 ...
2
votes
0answers
133 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: ...
6
votes
1answer
273 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?
9
votes
2answers
708 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 ...
4
votes
1answer
51 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 ...
1
vote
0answers
49 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 ...
8
votes
1answer
53 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
3answers
386 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 ...
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 ...
6
votes
0answers
53 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 ...
2
votes
2answers
83 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 ...
1
vote
1answer
82 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 ...
4
votes
2answers
60 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?
12
votes
1answer
5k 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 ...
9
votes
3answers
369 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 ...