PrimerIdent---一个基于web的保守引物设计工具(3)

时间：2026-01-18

Issue 2

Database

Output:

PrimerIdent runs the Primer3 core in the background against the template sequence assigned in the web form, listing all possible primers for the template sequence, using the criteria submitted in the web interface by the user.

PrimerIdent will then calculate the identity of all the primers from that list to each sequence included in the alignment and renders a final HTML report with the list of all primers depicting for each one the identities calculated for each sequence and a colour encoded pattern for easy interpretation (Figure 2).The colour code reflects the degree of identity of each primer to the aligned sequences. The colour variation is a function of the identity match using the following references: 0% identity corresponds to the colour pink, 50% to red, 90% to yellow and 100% to green.The resulting PrimerIdent report can then be used to easily find a primer with a specific identity pattern that will suit the needs of the researcher. In the case of the sample report shown in Figure 2, PrimerIdent easily depicts primers with a high identity to Catalase 1 (CAT1) sequences and simultaneously an identity as low as possible for Catalase 2 (CAT2).

The HTML report includes useful information about the designed primers: their position in the alignment, size, melting temperature, GC percentage, 3’ self-complementarity and any self-complementarity. This additional

information helps researchers to choose the best primer for a certain application if more than one primer with the identity pattern that suits their needs is found. If a primer pair is required, then the researcher will have to get separate reports for left and right primers, see what primers have the identity pattern needed and choose the pair based on the primer position included in the report.

Acknowledgements:

The authors wish to thank the Systems Management and Computation Unit, (Digital University Department, Reitoria – University of Porto), especially to José António Sousa and Anabela Vieira for providing and supporting the web hosting facilities for http://primerident.up.pt.

References :

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[2] SF Altschul et al. J Mol Biol (1990), 215:403-410 [PMID: 2231712] [3] S Rozen & H. Skaletsky Methods Mol Biol (2000), 132:365-86

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[4] JD Thompson et al. Nucleic Acids Res (1994), 22:4673-80 [PMID:

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Edited by P. Kangueane

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

License statement: This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial