5
votes
3answers
152 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
1
vote
1answer
112 views

What are the differences between HPRD and BIOGRID databases?

What are the differences between HPRD and BIOGRID protein-protein interactions databases? What are their purposes? Why do we need two different databases? How is data collected into each one? How ...
1
vote
0answers
37 views

Workflow for batch analysis of ROI in histology samples

This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via ...
3
votes
1answer
91 views

Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...
0
votes
0answers
240 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 ...
4
votes
1answer
189 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
334 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 ...
2
votes
0answers
137 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
3answers
94 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 ...
4
votes
2answers
133 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
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?
3
votes
2answers
224 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 ...
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: ...