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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What does conditional analysis of a SNP in a GWA study entail?

I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
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2answers
258 views

Confusion related to gene expression

I have a set of gene expression data downloaded from http://www.ncbi.nlm.nih.gov/geo. I have two sets of data, one is the raw probe intensity data set in the form of CEL files. Another is processed ...
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55 views

How can I obtain a computer readable model of Dr. Gerhard Michal's biological pathways map?

I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is ...
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30 views

Choice of Molecular markers to carry out molecular phylogenetics

For evolutionary analysis of different individuals within a population, the preferable molecular markers are non-coding regions of mitochondrial DNA. My question is that why they are used what is the ...
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37 views

Identifiying a conserved residue in multiple PDB structures

I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them. Originally I wanted to extract the sequences from the PDB files with ...
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80 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page ...
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55 views

Multistability in the lactose ultization network

Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram". ...
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128 views

Simplified molecular-input line-entry system

This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer. What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is ...
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1k views

How to check if a fastq file has single or paired end reads

I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method? I checked wikipedia and MAQ but I want to know if is there a reliable document ...
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55 views

RNA-seq Data on domestic animal with different environment

I want to find the RNAseq data available on domestic animals in different environments. If microarray data is available, it would be more useful. If you know I would appreciate to inform me.
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How to calculate extent of Sequence similarity [closed]

I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity. I have a Problem Statement: we have a sensor ...
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1answer
337 views

How does MEME compute the background frequency of nucleotides?

I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested. I would like to know how MEME estimates the background ...
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380 views

Software for counting fly eggs

Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
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72 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 ...
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147 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 ...
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83 views

How to get the correct RefSeq Protein transcript for a given RefSeq Nucleotide transcript?

How to get versioned Protein Accession Number for a Refseq Accession Number? I have some versioned RefSeq Accession numbers and I would like to know their corresponding Protein Accession Numbers. ...
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182 views

How could I identify whether given RNA-seq data is paired end or single end

I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702 ftp and downloaded sra file. ...
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200 views

Epistasis Across Chromosomes and Individuals 'Homozygous for Interactions'

Apologies for any failures in nomenclature. I'm a mathematician who is making a foray into genetics for a masters thesis. Specifically, I'm generating artificial diploid genetic sequence data and ...
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2answers
311 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
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174 views

Is it possible to dock multiple ligands with the target?

Is it possible to dock multiple ligands with a target? If so, what is the suitable software used for? -- Is it possible to fix specific docking region for the target (or) automatic?
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124 views

Publicly available resources for learning metagenomics

We are starting a metagenomics project in our research group to study microbiota in the respiratory tract. Since the are no books yet about metagenomics, seems reading some reviews and online ...
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228 views

Plotting metabolic networks?

I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes ...
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1answer
92 views

relative-rate of evolution

I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short ...
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2answers
136 views

Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...
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60 views

Finding RNA Loops

I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even ...
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285 views

What makes a DNA sequence motif a DNA sequence motif?

I've read about DNA sequence motifs, but still don't understand what makes some sequence a DNA sequence motif. Is this a well-defined concept? For, example, What are DNA sequence motifs? says: ...
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106 views

Combining gene expression data from two species

I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
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103 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, ...
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Where can I find histograms and tables of prevalence of mutations in cancer?

At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was ...
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126 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: ...
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1answer
61 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 ...
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1answer
46 views

How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

I have a list of taxids that looks like this: 1204725 2162 1300163 420247 I am looking to get a file with taxonomic ids in order from the taxids above: ...
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2answers
85 views

What are sources for learning bioinformatics for self-learning?

What are the sources for learning bioinformatics(books, websites/MOOCs)? Does it require prior knowledge of programming language because I am a complete noob when it comes to programming language.
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76 views

Statistics on energy consumption breakdown per biological functions across organisms?

Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of "Bacteria spend X% of energy on information processing, Y% for ...
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How do I view the simulated protein structure along with ligand in VMD?

I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
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54 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 ...
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How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
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Which sequence assemblers I can use to compare different paradigms?

I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn). I ...
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Are there any de-novo genome assembly programs for HADOOP?

I have access to a small (approx 20 nodes) cluster that has HADOOP running on it, and I need to do some de-novo genome assembly. I'd like to ask is anyone knows of any program that can do this on a ...
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301 views

Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA [closed]

We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The ...
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2answers
220 views

Biological key file format

I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data. Thanks
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0answers
168 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 ...
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2answers
210 views

High sequence similarity but start codon isn't methionine

I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is ...
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3answers
621 views

Bioinformatics tool for “pairwise alignment” of complementary sequences?

I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate ...
3
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1answer
146 views

What is the last heavy atom of an amino acid?

I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it ...
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1answer
97 views

What information can Uniprot give me about phosphorylated forms of proteins?

I have a list of proteins formatted like this: ...
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1answer
734 views

Ka/Ks (dN/dS) analysis module for Python?

From this wiki article: In genetics, the Ka/Ks ratio (or ω, dN/dS), is the ratio of the number of Nonsynonymous substitutions per non-synonymous site (Ka) to the number of synonymous ...
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2answers
489 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 ...
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142 views

Is there a database of cell images?

We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone ...
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Construct Phylogeny form Edgelist

I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form: ...