Computer programs that aid in the storage, processing, and analysis of biological data.

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47 views

Software to calculate Fst from sequence data

I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations ...
6
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1answer
135 views

What is the best file format to store gel images?

I store many gel images which are included in my Latex notebooks. The geldoc software normally produces TIFF files, however, Latex only accepts PNG or JPEG. If I am going to store only a single copy ...
3
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1answer
45 views

How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
3
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0answers
39 views

Visualisation of phylogeography

I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the ...
2
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6answers
160 views

Sequence analysis software suites

I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what ...
3
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1answer
122 views

For people who work in microbiology labs, what software do you use to manage your strains?

It's just a small microbiology lab that currently records everything on paper, and there's quite few mutants as well. Is Excel commonly used for this sort of thing? Or is there a better software to ...
5
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3answers
162 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]: ...
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1answer
154 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 ...
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0answers
54 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 ...
7
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2answers
272 views

Free software for measuring parts of an image?

Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? ...
1
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1answer
82 views

Statistical Analysis of Protein Folding Problem [closed]

I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (Introduction to Protein Structure Prediction: Methods and Algorithms). Does anyone ...
3
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1answer
94 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 ...
4
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1answer
203 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
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1answer
408 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
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0answers
163 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
2answers
264 views

What would it take to recognize a deer by its photo?

I am trying to recognize a deer by its antlers or any other means. Elaborating: I was hoping to use their antlers to recognize them but I have heard that most deers shed their antlers every year so ...
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0answers
22 views

Do the antlers re-grow in the same pattern every year? [duplicate]

I am a software engineer and I am trying to develop a system to identify a deer by its photograph. Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern ...
2
votes
3answers
104 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
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2answers
150 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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1answer
1k views

3D models of adult male brain in the Blender software? Any open-sourced version for research?

I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale here but because I am researching I would ...
8
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1answer
162 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
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2answers
258 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
87 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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0answers
56 views

bam viewer that works on authenticated ftp urls with username/password combination? [closed]

Are there any BAM file viewers that will work on authenticated ftp urls with username/password combination? For example, something like this: ...
1
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1answer
834 views

Is there a free alternative to Gelcompar for comparing banding patterns across multiple gels?

In order to run my microbial community samples from my experiments through DGGE, I was required to use multiple gels. Thus it is necessary to compare banding patterns across more than one gel. ...
5
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2answers
52 views

tools to reconstruct the transcriptional regulatory circuits?

What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?
4
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1answer
196 views

Automatic cropping of collimated digital X-ray images

Do you have any suggestions for a library which offers an algorithm to crop digital X-ray images automatically? We receive full-size images (43x43cm) from a detector, independent of the collimator ...