militriple.blogg.se - Amplifx pcr

#AMPLIFX PCR SOFTWARE#
#AMPLIFX PCR CODE#
#AMPLIFX PCR DOWNLOAD#

#AMPLIFX PCR CODE#

For advanced users, they may look at our Python code for details.įig. We use the following Python-like seudo-code and Fig. The “index process” is to store all the positions of all k-mers which appears in all the sequences from a FASTA format database. For example, "AAATTTCCC" is a mer with k=9. A “k-mer" is defined as a short DNA sequence with a length of k nucleotides. I will explain in details.įirst of all, I have to explain the "k-mer".

So, what is the "k-mer index algorithm"? And why this algorithm can't miss possible binding sites? Because MFEprimer-2.1 pre-stored all the positions of all k-mers. Even we carefully handled these options, we still found many less significant hits were missed. The reasons are 1)BLAST only reports the significant hits in statistically 2) the BLAST output was controlled by "-E" and other options. But we found that BLAST may lose many less significant hits. Someone may think that what if let BLAST do the first step (find all the possible binding sites)? Actually, MFEprimer 1.x version uses this strategy. So the first step we have to do is to find all the possible binding sites with the k-mer index algorithm], and then to evaluate the binding stability using the Nearest-Neighbor model. For example, the mismatch "G-G" contributes as much as the Gibbs free energy of -2.2 kcal/mol to the duplex stability. They bind to each other just because they are stable in thermodynamics, not because they are matched in base pairs. However, the annealing process of primer and its target sequence is thermodynamics. As we know that, BLAST is a famous program to find the homology sequence from a database by sequence similarity. This is the speed problem I have to solve, while, the other question force me MUST to replace the BLAST. Unlike MFEprimer 1.x versions, which use BLAST for primer binding sites search, MFEprimer-2.1 uses the k-mer index algorithm to speed up the primer binding sites search process. Run MFEprimer and you will get the results if not errors found.Index the database, it will create three files with suffix.

#AMPLIFX PCR DOWNLOAD#

psutil (>= 3.0.0): download from here ( ).

The MFEprimer-2.1 server does not require a login and is freely available at. In addition, the databases supported by MFEprimer-2.1 are comprehensive, and custom databases can also be supported on request. Analyses for degenerate primers and multiple PCR primers are also supported in MFEprimer-2.1. Based on these characteristics and the user-friendly output, users can readily draw conclusions about the specificity of PCR primers. Several important characteristics such as the sequence, melting temperature and size of each amplicon, either specific or non-specific, are reported on the results page. MFEprimer-2.1 uses a k-mer index algorithm to accelerate the search process for primer binding sites and uses thermodynamics to evaluate binding stability between each primer and its DNA template. The MFEprimer-2.1 server allows users to check primer specificity against genomic DNA and mRNA/cDNA sequence databases quickly and easily.

#AMPLIFX PCR SOFTWARE#

The original software can be found at IntroductionĮvaluating the specificity of PCR primers is an essential step in PCR primer design. NOTE: This software has been edited in order to make it installable on Linu圆4 via setup.py A fast thermodynamics-based program for checking PCR primer specificity