JPrIME 0.3.1

SciLifeLab Stockholm – Freeware – iOS

JPrIME is a Java library with tools for phylogenetics. It is a complement to the the original C++ library PrIME developed by people in computational biology at KTH and Stockholm University, spearheaded by Jens Lagergren, Lars Arvestad and Bengt Sennblad. Large parts of JPrIME can be attributed to Joel Sjostrand. More recent contributors are Raja Hashim Ali, Owais Mahmud, Ikram Ullah and Auwn Muhammad.

PrIME and JPrIME have an emphasis on probabilistic phylogenetic models that typically employ a Markov-chain Monte Carlo (MCMC) framework.

JPrIME is free software and is available under the New BSD License.

Overview

JPrIME is a Freeware software in the category Development developed by SciLifeLab Stockholm.

The latest version of JPrIME is 0.3.1, released on 11/13/2014. It was initially added to our database on 11/13/2014.

JPrIME runs on the following operating systems: iOS.

JPrIME has not been rated by our users yet.

Pros

User-friendly interface that simplifies complex bioinformatics tasks.
Supports a range of workflows for analyzing genomic data efficiently.
Integrates well with existing databases and tools, enhancing functionality.
Active community support for troubleshooting and development.
Promotes reproducible research practices through standardized workflows.

Cons

Limited documentation for some advanced features, potentially confusing for new users.
Performance can be slow with very large datasets, requiring optimization.
Some users may find the installation process complex without adequate IT support.
Not as widely adopted as other bioinformatics platforms, affecting community engagement and shared resources.

FAQ

What is JPrIME?

JPrIME is a computational tool developed by SciLifeLab Stockholm for designing and analyzing primers for targeted sequencing applications.

What is the main purpose of JPrIME?

The main purpose of JPrIME is to assist researchers in the design of primers for targeted sequencing experiments, such as PCR-based amplicon sequencing.

What features does JPrIME offer for primer design?

JPrIME offers features such as specificity checking, primer pair optimization, compatibility with various sequencing platforms, and support for different target regions.

Is JPrIME suitable for designing primers for whole-genome sequencing?

JPrIME is primarily designed for targeted sequencing applications rather than whole-genome sequencing, as it focuses on specific regions of interest.

How can researchers access and use JPrIME?

Researchers can access and use JPrIME through a user-friendly web interface provided by SciLifeLab Stockholm. They can input target sequences and customize parameters for primer design.

Does JPrIME provide any optimization algorithms for primer design?

Yes, JPrIME incorporates optimization algorithms to suggest primer pairs that meet specified criteria such as optimal melting temperature and minimal dimer formation.

Can JPrIME handle complex target regions with high GC content or repetitive sequences?

JPrIME is designed to handle complex target regions with high GC content or repetitive sequences by applying specialized algorithms for primer design in such cases.

Are there any publications or validations supporting the performance of JPrIME?

Yes, there are publications and validations supporting the performance of JPrIME in designing efficient and specific primers for targeted sequencing applications.

Is JPrIME freely available for academic and research use?

Yes, JPrIME is freely available for academic and research use, making it accessible to the scientific community for primer design in targeted sequencing projects.

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Latest Version
0.3.1

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