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PrimerIdent: A web based tool for conserved primer design



Alberto M Pessoa1,2*, Susana Pereira 1,2, Jorge Teixeira1,2



1University of Porto, Faculty of Sciences, Biology Department, Edifício FC4, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal; 2BioFIG - Center for Biodiversity, Functional & Integrative Genomics, Plant Molecular Biology & Biotechnology Lab, University of Porto, Portugal


E-mail*; * Corresponding author


Article Type






received  May 28, 2010; accepted  June 9, 2010; published online July 06, 2010




Conserved primers across multiple species and simultaneously specific for a certain isozyme can be rare and difficult to find. PrimerIdent was developed aiming to automate this primer design and selection process in a given nucleotide sequence alignment, providing an intuitive, easy to interpret graphical result, which offers a list of all possible primers that meet the user criteria, with a colour-code identity to each sequence in the alignment. The software here presented is a simple and intuitive web based tool that is suitable for distinguishing very similar nucleotide sequences, such as isozymes-coding sequences, to enable the conserved primer design across multiple species, necessary for approaches that rely on knowing if a primer is suitable for a certain set of pre-aligned sequences, to design a specific primer to a certain sequence variation, or a combination thereof. This extremely useful software can, therefore, be used as a tool for the specific amplification of individual members of multigenic families across related species and also to evaluate the differential expression of isogenes for a given species.







Primer design, conserved primers, multiple-purposed primers, gene-specific primers




Subramanian et al. Bioinformation 5(2): 52-54 (2010))


Edited by


P. Kangueane








Biomedical Informatics




This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.