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.
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3answers
94 views
How to create a collection of anonymous sequences for teaching and testing? [closed]
I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection.
The sequence files would be used for teaching and for testing ...
4
votes
2answers
56 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?
4
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2answers
99 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 ...
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 ...
4
votes
1answer
96 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 ...
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 ...
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 ...
4
votes
2answers
66 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 ...
4
votes
1answer
38 views
How to get smallest subtree containing a set of nodes from BioPhylo?
I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and ...
4
votes
1answer
115 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 ...
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:
...
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 ...
4
votes
3answers
80 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 ...
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
2answers
82 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
4
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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 ...
3
votes
2answers
53 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 ...
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 ...
3
votes
1answer
47 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 ...
3
votes
2answers
117 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
53 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 ...
3
votes
1answer
56 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 ...
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 ...
3
votes
1answer
121 views
Multiple sequence alignment - how to align everything to 1 gene sequence?
I'm having trouble aligning 3 sequences together - the total gene (~2500bp) and the forward and reverse sequences that are ~1000bp in length. Now I'm using Clustal X2, but the problem is that the ...
3
votes
1answer
240 views
Displaying nucleotide at a single position from RNA-seq reads in a BAM file
How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am ...
3
votes
1answer
45 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 ...
3
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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 ...
2
votes
2answers
65 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 ...
2
votes
1answer
60 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
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 ...
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 ...
2
votes
3answers
45 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
40 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
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 ...
2
votes
1answer
97 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
108 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
2
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0answers
60 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 ...
2
votes
0answers
26 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 ...
2
votes
3answers
78 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 ...
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 ...
2
votes
0answers
109 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:
...
2
votes
0answers
142 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 ...
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 ...
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 ...
1
vote
1answer
78 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 ...
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, ...
1
vote
2answers
93 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 ...
1
vote
1answer
25 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 ...
1
vote
1answer
27 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 ...
