### Citations

1248 | On the statistical analysis of dirty pictures,”
- Besag
- 1986
(Show Context)
Citation Context ...ution over the range of possible homolog mappings. We then formulate the homology assignment problem as a labeling problem for a special class of Markov networks known as the ferromagnetic Ising model=-=[2]-=-. This allows us to take advantage of recently developed efficient linear programming algorithms for exact inference[10]. We delineate the sequence matching from the homology mapping aspects of alignm... |

317 | Multi-Camera Scene Reconstruction via Graph-Cuts,”
- Kolmogorov, Zabih
- 2002
(Show Context)
Citation Context ...lem for a special class of Markov networks known as the ferromagnetic Ising model[2]. This allows us to take advantage of recently developed efficient linear programming algorithms for exact inference=-=[10]-=-. We delineate the sequence matching from the homology mapping aspects of alignment, and outline the following approach to homology mapping: (1) Obtain matches (not necessarily identical) between mult... |

216 |
Human–mouse alignments with BLASTZ.
- Schwartz, Kent, et al.
- 2003
(Show Context)
Citation Context ...) homology mapping: separating matches into homologous components and chance occurrence of similarity. Alignment methods such as BLAST, BLAT and BlastZ focus on sequence matching, not homology mapping=-=[1, 9, 11]-=-. Typically, exact matches are identified using suffix trees, and are then extended locally to form alignments that are constrained to preserve the sequence ordering. The number of local alignments pr... |

28 |
Mavid multiple alignment server
- Bray, Pachter
- 2003
(Show Context)
Citation Context ...ext. Specifically, by coherency we mean general preservation of order and orientation among nearby matches with rearrangement where necessary to maximize collinearity. Recent anchor based approaches (=-=[8, 3, 5, 7]-=-) obtain local alignments using BLAST-like methods, and provide a subsequent homology mapping step applied to the local alignments using dynamic programming algorithms or heuristics. The methods produ... |

14 |
BLAT - the BLAST like alignment tool
- Kent
(Show Context)
Citation Context ...) homology mapping: separating matches into homologous components and chance occurrence of similarity. Alignment methods such as BLAST, BLAT and BlastZ focus on sequence matching, not homology mapping=-=[1, 9, 11]-=-. Typically, exact matches are identified using suffix trees, and are then extended locally to form alignments that are constrained to preserve the sequence ordering. The number of local alignments pr... |

1 |
al.: Basic local alignment search tool
- et
- 1990
(Show Context)
Citation Context ...) homology mapping: separating matches into homologous components and chance occurrence of similarity. Alignment methods such as BLAST, BLAT and BlastZ focus on sequence matching, not homology mapping=-=[1, 9, 11]-=-. Typically, exact matches are identified using suffix trees, and are then extended locally to form alignments that are constrained to preserve the sequence ordering. The number of local alignments pr... |

1 |
al.: Glocal alignment
- et
(Show Context)
Citation Context ...uristics. The methods produce pairwise global alignments. Some extend to multiple alignment. Shuffle-LAGAN segments two sequences into a globally coherent alignment that locally preserves collinearity=-=[6]-=-. 1 JGG in Bioengineering, University of California, Berkeley. caspian@compbio.berkeley.edu 2 Department of Mathematics, University of California, Berkeley. lpachter@math.berkeley.edu 1s2 Figure 1: BL... |

1 |
al.: Efficient multiple genome alignment
- et
(Show Context)
Citation Context ...ext. Specifically, by coherency we mean general preservation of order and orientation among nearby matches with rearrangement where necessary to maximize collinearity. Recent anchor based approaches (=-=[8, 3, 5, 7]-=-) obtain local alignments using BLAST-like methods, and provide a subsequent homology mapping step applied to the local alignments using dynamic programming algorithms or heuristics. The methods produ... |