What bioinformatics parameters should be used to justify the specificity?

01 January 2014 1 6K Report

I am developing a molecular diagnostic method and I would like to justify the specificity using bioinformatics tools like BLAST or Clustal, as I have no access to DNA from different species. What parameters are most representative?

Thanks and regards

Rashad Abdul-Ghani

I understand that you want to design a specific primer pair. You can use Primer-BLAST, where under the parameter of checking primer specificity, you can choose the source organism (This is Homo sapiens by default) and then select the nucleotide sequence database you want to search within. If you use the non-redundant (nr) database, this will cover a broader range of several databases, including GenBank and EMBL. However, you can select the database you are interested in.

Kind regards!

Badges
Science topic

More Javier Gandasegui's questions See All

It is possible to obtaing high-quality DNA from urine samples preserved with forlmol?

Hello, I want to know if it is possible to obtaing high-quality DNA to amplify schistosome-DNA in urine samples previosly preserved with formol 1%. Thanks

07 August 2017 9,741 1 View

Is it possible to diagnose STH and schistosome infections by microscopy in forzen samples of feces?

Hello, I want to know if STH and schistosome eggs are resistant to freezing and can be detected a second time if forzen feces are reanalyzed by the Ritchie concentration method and Kato-Katz. Thanks.

07 August 2017 4,023 11 View

What is the best method to validate molecular or any diagnostc test?

Hello; I am trying to validate or asses the diagnostic reliability of a new test. I have doubt about the necessary number of samples, the comparison between the different diagnostic test employed...

31 December 2015 4,896 4 View

Waht are the best methods for sample collection and storage for DNA extraction?

Hello! We are preparing an study for molecular diagnosis in different type of spicemen: blood, feces and urine. The samples are collected in a different country and we want to avoid the cold...

31 December 2014 2,799 5 View

Does anyone know how much DNA is in a Schistosoma egg?

I am conducting a molecular diagnostic technique for S. haematobium and I would like to know how much DNA is in an egg and in which paper I can find this information.

03 April 2014 1,257 2 View

What is the best method for DNA extraction from a filter?

Hello, My goal is to filter water with different biological forms and make a DNA extraction from the filter. The technique must be simple and cheap, so I'd like to use a paper filter but I could...

02 March 2014 7,820 5 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How do I increase the yield of my PCR product?

Hello, We would like to increase the yield of our PCR product. We are running a series of PCR reactions that is targeting ~1.1kb sequence. We begin each reaction with ~400pg of template DNA...

02 March 2021 4,029 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View