Gemi: PCR Primers Prediction from Multiple Alignments

Haitham Sobhy,Philippe Colson

doi:10.1155/2012/783138

Abstract

Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size.

Highlights

Polymerase chain reaction (PCR) has been increasingly used over the last two decades to detect, quantify, and/or sequence nucleic acids from various sources [1, 2]
The number of publications in PubMed referencing “PCR” has increased from 2846 in 1990 to 20,426 in 2000 and 44,231 in 2010. This method has a wide range of applications, in the field of microbiology [3,4,5] where primers and probes are often designed with the aim to hybridize to the greatest number of genome sequences for given groups of viruses, bacteria, or parasites [5,6,7]
Designs can be challenging if primers and probes are meant to hybridize to sequences with considerable nucleotide diversity; the task becomes more complicated as the nucleotide diversity increases

Summary

Introduction

Polymerase chain reaction (PCR) has been increasingly used over the last two decades to detect, quantify, and/or sequence nucleic acids from various sources [1, 2]. The number of publications in PubMed referencing “PCR” has increased from 2846 in 1990 to 20,426 in 2000 and 44,231 in 2010 This method has a wide range of applications, in the field of microbiology [3,4,5] where primers and probes are often designed with the aim to hybridize to the greatest number of genome sequences for given groups of viruses, bacteria, or parasites [5,6,7]. We present Gemi, which means “to find” in ancient Egyptian, a simple, automated, fast, and versatile tool to find universal primers and probes within a set of multiple, variable, and long sequences. We believe that our tool can be useful in the field of microbiology

Algorithm and Method

Results and Discussion

Availability and Implementation

Conclusions