Universal fingerprinting chip server

• Published in: Bioinformation Vol. 8; no. 12; pp. 586 - 588
• Main Authors: Casique-Almazán, Janet, Larios-Serrato, Violeta, Olguín-Ruíz, Gabriela Edith, Sánchez-Vallejo, Carlos Javier, Maldonado-Rodríguez, Rogelio, Méndez-Tenorio, Alfonso
• Format: Journal Article
• Language: English
• Published: Singapore Biomedical Informatics 01-01-2012
• Subjects: Server; virtual hybridization; microarray; Fingerprinting; phylogenetic; universal
• ISSN: 0973-8894; 0973-2063; 0973-2063
• DOI: 10.6026/97320630008586

The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence, including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off value, it is considered as a site of high probability of hybridization. The Universal Fingerprinting Chip Applications Server contains the software for visualizing predicted hybridization patterns, which yields a simulated hybridization fingerprint that can be compared with experimentally derived fingerprints or with a virtual fingerprint arising from a different sample.
The database is available for free at http://bioinformatica.homelinux.org/UFCVH/