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
55 views
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 ...
0
votes
0answers
16 views
best known indexing method / transformation to coordinates for gene sequences
What would be the best known method to transform a gene or proteine sequence to some coordinate space (so $t(G)$ is the transformed sequence) complying to following rules:
similar sequences ...
-1
votes
0answers
19 views
Is there any problem in the debian package of BLAST executables downloaded from UBUNTU software centre? [closed]
I am using standalone BLAST in my two computer. The executables are installed differently in these two machines. In one case blast2 package has been installed from UBUNTU software centre which is a ...
1
vote
1answer
26 views
Mapping a mutation to known SNP, 3' UTR, miR
I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information.
The ssm is in the following format:
...
0
votes
0answers
28 views
Is there any interest to searching for intelligent messages within the DNA coding sections already responsible for coding RNA to make proteins? [duplicate]
Is there any major flaws in the below reasoning that would not make it worthwhile to find a potential intelligent message inside our DNA? I'm thinking modern science would shy away from this endevour ...
2
votes
2answers
45 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 ...
0
votes
0answers
25 views
Reverse complement of reconstruction model for assembling reads
One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
0
votes
1answer
54 views
TCGA data, and bioinformatics design questions for SNP/ mirna analysis
It's my first time posting to this forum but was looking for some help on the data aspects of this project.
My tools of choice would be in python/R .
Goal: I'm looking to create a disease specific ...
4
votes
3answers
90 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 ...
0
votes
0answers
29 views
Modeller - Convert FASTA to PIR
I am doing a basic modelling following the instructions here. But different target / template sequences.
http://salilab.org/modeller/tutorial/basic.html
Do I need to convert the FASTA to PIR with a ...
0
votes
1answer
28 views
SNPs mapping into protein
Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means?
1
vote
0answers
29 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?
4
votes
1answer
100 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 ...
15
votes
3answers
436 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?
1
vote
1answer
47 views
Is there a way to see what representations are currently displayed in PyMOL?
I am using PyMol to visualize .pdb protein structures.
I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
6
votes
2answers
115 views
BLAST DNA Sequences Reversed
I have been trying to learn some basic DNA sequencing techniques and have been using BLAST as a reference. I thought that I was starting to get it, but then I cam across this:
It looks like it's ...
1
vote
1answer
79 views
Chemical structure prediction
I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure ...
2
votes
3answers
47 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 ...
6
votes
3answers
178 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 ...
2
votes
3answers
83 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 ...
1
vote
1answer
77 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, ...
0
votes
0answers
34 views
Confusion related to the use of PCA to determine the background network
I was reading this paper related to use of gene expressions for predicting the drug response. I have this confusion, the paper has used PCA on the covariance matrix formed by the genes to get what is ...
2
votes
0answers
62 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 ...
0
votes
2answers
49 views
Deterministic model of lambda-phage lysis/lysogeny [MATLAB]
Project 1 Base:
Can someone please help me understand what I need from Project 1 Base code to do questions 1 and 2 from the first image? I'm new to MATLAB so a thorough explanation would be ...
2
votes
0answers
27 views
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 ...
1
vote
1answer
79 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' ...
0
votes
0answers
36 views
Choosing biology course for minor in computation biology [closed]
I apologize if this question is not right for this forum. I will be transferring to UC Davis where I will be majoring in computer science. I'm considering specializing in scientific computation and ...
2
votes
1answer
71 views
Expanding the SETI initiative to seek intelligent data within DNA sequences?
I've recently read a couple articles dealing with long term data storage, and DNA was suggested as one of the prime candidates for long term storage of digital data additionally, there is this article ...
2
votes
1answer
43 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
23 views
ChIP-seq and the output of SPP
I have been processing some ChIP-seq data with the R package spp. I looked through the literature (ENCODE uses it) and it seemed that spp is indicated as a good program to use. I have found and ...
-3
votes
2answers
84 views
Specific enzyme for C. elegans [closed]
We are looking for an enzyme that appears in C. elegans but isn't common for: human, Drosophila or mouse.
We need it for a little research project, thanks for your help!
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 ...
11
votes
1answer
280 views
Looking for a cancer drug target database to guide sequencing of patient tumor DNA
I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s ...
3
votes
2answers
57 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 ...
5
votes
3answers
369 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 ...
0
votes
0answers
26 views
Recombination-based vs. Sequence-based genetic mapping
Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?
I think that in the past recombination-based ...
1
vote
2answers
96 views
Batch convert miRNA names to Accession IDs?
Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters.
EDIT: both @rg255 and @shigeta have ...
4
votes
2answers
67 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 ...
4
votes
1answer
82 views
Can forensic DNA analysis be used to generate a visual approximation of a suspect?
In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
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, ...
3
votes
1answer
73 views
What is benjamini
I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some ...
7
votes
5answers
198 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 ...
4
votes
2answers
83 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
2
votes
1answer
30 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 ...
3
votes
1answer
54 views
Difference between “transcriptional activity” and “RNA expression”
I am working with a network object where the nodes are different events in molecular biology.
Specifically;
Catalytic activity of X,
RNA expression of X,
GTP-bound activity of X,
Kinase activity of ...
4
votes
2answers
101 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 ...
9
votes
1answer
121 views
Systems identification in small neural network
When analyzing data from cortex, we often try to understand what each neuron does in terms of its inputs from other neurons - a specific kind of a systems identification strategy. Most current ...
1
vote
1answer
57 views
What is the best way to read and normalize large amounts of Agilent data into R? [closed]
I have a large amount of Agilent data (580 text files that are ~200 MB in size each) that I'd like to normalize. I've run into a problem in that my machine (with 8 GB of memory) still runs out of ...
6
votes
1answer
82 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 ...
10
votes
4answers
192 views
What can you tell about a person, having only their whole genome as information?
Well, the question is in the title, no explanation need.
