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A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes |
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| Authors: | Anne-Kathrin Schultz Ming Zhang Thomas Leitner Carla Kuiken Bette Korber Burkhard Morgenstern Mario Stanke |
| Institution: | 1. Institute of Microbiology and Genetics, University of G?ttingen, Goldschmidtstr. 1, 37077, G?ttingen, Germany 2. Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA 3. The Santa Fe Institute, Santa Fe, NM, 87501, USA |
| Abstract: | BackgroundJumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events. |
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