Related Experiment Video
Updated: Jun 23, 2026

Interview: HIV-1 Proviral DNA Excision Using an Evolved Recombinase
Published on: June 16, 2008
jpHMM: improving the reliability of recombination prediction in HIV-1
Anne-Kathrin Schultz1, Ming Zhang, Ingo Bulla
1Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany.
Abstract:
Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of 'uncertainty' regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/.
Related Concept Videos
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Homologous Recombination
Homologous Recombination
Viral Recombination
Crossing Over

