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)

2
votes
1answer
1k views

What does phasing mean?

What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually ...
2
votes
3answers
1k views

Primer design for Gibson assembly

I'm trying to design a primer for Gibson assembly. My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid. I am unsure how to design my primers for ...
2
votes
2answers
97 views

Core Biological concepts explained to a Computer Scientist?

I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as: Evolution, Selection and Variation, to a ...
2
votes
1answer
30 views

Protein PTM site prediction

Is there any in silico analysis method to predict post-translational modification sites on a given protein?
2
votes
1answer
24 views

What are host cellular factors?

With respect to this paper: Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication What does the term "host cellular factors" mean??
2
votes
2answers
89 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
2
votes
1answer
42 views

Data Bias in protein-protein interactions data

Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?. a)The first is gene co-occurrence ...
2
votes
2answers
94 views

Where to find the corrected BLOSUM matrices?

I was looking at this paper which talks about the miscalculations in the BLOSUM matrices and how the "wrong" BLOSUM62 matrix performs better than the corrected version. I was trying to find the ...
2
votes
1answer
59 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
2
votes
2answers
101 views

chimeric sequences [closed]

I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. ...
2
votes
1answer
46 views

Number of autoregulation and FFL motifs in a network

Suppose we have a network with N* nodes (N* is the number of internal nodes). Every directed link in this network exists with probability p. What would be the number of: motifs that are ...
2
votes
2answers
60 views

Connection between genes and pathways

I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to ERBB2 as a gene and a pathway. I don't have solid biology background. What exactly means when we ...
2
votes
1answer
623 views

What do rs id, allele coded 0 and allele coded 1 mean?

So, for a project I've been working on (different story), I've been looking at the HapMap Project, and their free online files. In their README file, they talk about how for each legend file for each ...
2
votes
3answers
115 views

What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
2
votes
1answer
89 views

Confusion related to a term probe-by-background interaction

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, ...
2
votes
1answer
226 views

One flybase gene number (FBgn), many Affymetrix Id's

I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as ...
2
votes
1answer
145 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 ...
2
votes
1answer
61 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 ...
2
votes
2answers
59 views

Protein Structure Parameters

I'm wondering about the minimal set of parameters necessary to define a protein's structure. My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and ...
2
votes
2answers
96 views

What is the meaning of dots and dashes in clustalw?

I am converting outputs in stockholm format to clustalw using ...
2
votes
1answer
78 views

Whole genome sequence analysis software

Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, ...
2
votes
1answer
29 views

Gene Sequencing and Plasmapper

Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)? For information I would like to convey that I am using Plasmapper and BioJava for achieving ...
2
votes
2answers
82 views

Local BLAST Copy Number per Hit

I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at ...
2
votes
1answer
239 views

Difference between sequential and conformational epitope

Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through ...
2
votes
2answers
113 views

How do I perform recurring pattern mining or regular expressions of nucleotide sequences?

I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?
2
votes
1answer
268 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
2
votes
2answers
50 views

Hiding identical sequences in NCBI web interface

Sometimes there are identical sequences in Genbank/Genpept, most often coming from the same species but different strains. Ie if I look up "bacteria chitin synthase", the 624-aa protein from Dickeya ...
2
votes
2answers
83 views

Bioinformatics : Drawbacks of using ORA(Overlap Analysis)

What do you think are the potential drawbacks/weakness of using ORA to explain distinction between two phenotypes. I identified a few which were the dependencies of DE and the statistical method used ...
2
votes
1answer
249 views

How do PLINK files and HapMap Phased files differ?

I know that PLINK and HapMap files show the same information, but can you give a thorough explanation of how exactly they differ.
2
votes
1answer
55 views

How can I view modENCODE data faster?

I am trying to view several data tracks in the modENCODE GBrowse genomic browser. However, the site is so slow, it is practically unworkable. Is there a faster way to explore the data?
2
votes
1answer
853 views

Problems with analysis of small RNAseq data - Adapter trimming

I have always faced a problem while analyzing small RNAseq data, at the step of adapter trimming. Overview of small RNAseq (Illumina) RNA is size fractionated using columns or PAGE 3' and 5' ...
2
votes
1answer
60 views

Confusion related to the DAVID tool

I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I ...
2
votes
1answer
121 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 ...
2
votes
1answer
59 views

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
2
votes
1answer
45 views

Sequencing a specific region of a genome

First off, I'm new to bioinformatics and I am learning about DNA sequencing. Let's say that I knew that a specific region of a genome which contained information about a disease (whether it a person ...
2
votes
1answer
104 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook Probability Models for DNA Sequence Evolution by Durrett. In chapter 1, he discusses the Wright Fisher model and the coalescent theory ...
2
votes
1answer
43 views

Quantitative Comparisons of Phylogenetic trees

I am working on a broad phylogenomic analysis of proteins involved in one particular cellular process. I have constructed a phylogenetic tree for each protein. I am now working on comparing those ...
2
votes
1answer
103 views

Steps to confirm if predicted miRNA is good or bad

I aligned all miRNAs available to the supercontigs of a particular genome with certain parameters (e value of 0.01 and a word match of atleast 7 as suggested in this paper). I have also isolated the ...
2
votes
1answer
62 views

Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment

I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/) in nucleotide format. According to ...
2
votes
1answer
79 views

Comparing Shine Dalgarno scores, creating a distribution

I am in the process of creating a poster for the phage that I recently annotated. The phage is an A4 and the portion of the poster I am working on is analyzing the data that we have collected. I have ...
2
votes
2answers
85 views

Databases for metabolic pathways of human disease

Which databases contain the metabolic pathway of human diseases? I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.
2
votes
1answer
504 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 ...
2
votes
1answer
121 views

Transition/Transversion ratio

I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time ...
2
votes
2answers
125 views

Image analysis of GFP-tagged protein localization bursts

I'm reading an article (full text here) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent ...
2
votes
1answer
70 views

Is the book “Bioinformatics for Geneticists” outdated?

I am going to be working with genetics data in my organization's data warehouse next year and helping our biotechnology department. I work in academic research, but I have very little genomics ...
2
votes
1answer
111 views

.Net DNA/Codon Parser

Does anyone know of an .NET (C#,VB.NET, maybe F#) DNA parser? If not I will probably make one, it doesn't seem like it would be hard. My general idea was to generate something that would report the ...
2
votes
1answer
614 views

Molecular Evolution: Mrbayes never stops?

When I use my own data to build Bayesian phylogenetic trees using the software Mrbayes, after many generations, it never reaches stopping status (namely, the average standard deviation of split ...
2
votes
1answer
354 views

How to calculate or know by experiment the entropy of enzymes or protein?

How do you calculate or experimentally determine the entropy of enzymes or protein? In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy. Any references are ...
2
votes
1answer
513 views

Comparing BLAST and the Smith-Waterman algorithm

I've been asked: how does BLAST improve dynamic programming accuracy? I do know that BLAST is based on heuristic approach that approximates the Smith-Waterman algorithm and that the Smith-Waterman is ...
2
votes
1answer
257 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