Is there a way to determine single nucleotide polymorphisms using any bioinformatic tool?

10 October 2014 1 9K Report

I am looking to identify single nucleotide polymorphism nucleotide sequences to study how they have evolved/diverged from each other. Is there any bioinformatic tool to identify such changes in 2 or more sequences?

Guy Bottu

There is also the old Staden software (http://staden.sourceforge.net/). It takes as input capillary sequencer "trace" files and a reference sequence in EMBL format. It can make the distinction between SNP's and heterozygous differences and show you an alignment of the "traces".

Badges
Science topic

More Manan Vishvas Desai's questions See All

How to determine protein stability using GROMACS?

We wish to perform a molecular dynamics simulation of cell division protein from a hyperthermophile species at 37 deg cel to check for its stability. Is there a specific analysis in GROMACS for...

31 December 2016 7,717 18 View

What is importance of OXT atom found in aspartic acid? Does it participate in salt bridge formation?

During a molecular dynamics simulation i have found salt bridges being format being N(eta) atoms of Arg and OXT atom of Asp. What is the role of OXT atom and is such a salt bridge formation possible?

08 September 2016 10,161 3 View

Calcium as a chaotrope or kosmotrope?

Is calcium a chaotrope or Kosmotrope? The Hofmeister series shows it to be a kosmotrope, however, some sources refer to it as a chaotrope. Does it behave differently in biological systems as...

04 May 2016 4,391 4 View

What is meant by molecular or rotational tumbling of proteins?

Several computational models describe rotational tumbling and rotational relaxation time when describing protein motion and dynamics. What is meant by relaxation time and how is related tumbling?...

09 October 2015 4,252 5 View

Which is a more appropriate forcefield ff99IDP (AMBER) or OPLS for disordered proteins?

I wish to observe disorder-order transitions using MD. Which would be a more appropriate and accurate forcefield, ff99IDP (AMBER) or OPLS?

06 July 2015 3,511 4 View

What is the ideal time frame for molecular dynamics simulations?

I wish to observe helix-coil transformation using MD simulation. What would be the minimum time scale for the simulation to observe such conformational transitions?

06 July 2015 7,659 3 View

Is there a way to study peripatric speciation using bioinformatic approach?

Peripatric speciation as type of divergent evolution where a small subpopulation remains within the habitat of an original population but enters a different niche. Is there a way or a method of...

10 November 2014 2,418 1 View

How can I study the evolution of disordered proteins?

Is there as way or approach to understand and study the evolution of intrinsically disordered proteins based on their amino acid sequences using phylogenetics?

09 October 2014 1,739 3 View

What is the importance of glutamine in a protein's structure and function?

I have noticed that several microtubule-associated proteins contain stretches of glutamine residues. Is there a particular reason for the presence of such Q-rich regions?

09 October 2014 8,926 5 View

How did neurons evolve?

neurons are largely made of a cell body, dendrites and the axon. How did the neuron evolve into such a complex structure? Was the first neuron only a cell body and later developed axon and dendrites?

09 October 2014 7,256 0 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Self-Organizing Superorganisms—as envisaged by Nenad Sestan (2018)?

The rate of glucose consumption by the neocortex is reduced by over 80% during anesthesia (Sibson et al. 1998), which disables the synapses (Richards 2002) that are inundated by glial tissue (Engl...

08 August 2024 3,118 0 View

Is there any way to quantify bacterial and fungal cells in their mixed culture?

I am working in fungal fermentation of soybean meal and there is bacterial growth in them at times. I am trying to quantify fungal cell counts and bacterial cells; but I haven't been able to do at...

07 August 2024 7,535 4 View

The Bigger You Are, the Harder You Fall (some lessons from Dinosaurs)?

Evolutionary fitness is based on an organism’s ability to adapt rapidly to changing environmental circumstances. Large-bodied mammals have been equipped with large brains (and hence a high...

06 August 2024 4,849 2 View

Measuring the Intelligence of a Species?

Larger brains, which typically contain more neurons, store and transfer more information (Tehovnik and Chen 2015), but the precise relationship between number of neurons and information has yet to...

05 August 2024 1,238 2 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How is the bacterial genome's high protein count verified as genuine despite 800+ contigs and good metrics (98.55%completeness, 0.68% contamination)?

Given that the bacterial genome has over 800 contigs, but its quality metrics are good, with a completeness of 98.55% and a contamination of 0.68% as assessed by CheckM, what specific validation...

01 August 2024 1,514 1 View

The Origin of Human Language?

I attended a lecture at the Baylor College of Medicine (~ 2019) where one of the questions was “Does birdsong have anything to do with human language?” Noam Chomsky would say, “Absolutely not!”...

31 July 2024 1,706 4 View