Algorithms for restriction map comparisons

Algorithms for restriction map comparisons

An algorithm is presented which compares two restriction maps, yielding a measure of distance between the maps and relating the maps by an alignment. This new algorithm finds the minimum weighted sum of genetic events required to convert one map into the other, where the genetic events are the appearance/disappearance of restriction sites and changes in the number of bases between restriction s...

Dynamic programming algorithms for restriction map comparison

For most sequence comparison problems there is a corresponding map comparison algorithm. While map data may appear to be incompatible with dynamic programming, we show in this paper that the rigor and efficiency of dynamic programming algorithms carry over to the map comparison algorithms. We present algorithms for restriction map comparison that deal with two types of map errors: (i) closely s...

White Pattern based map comparisons

Map comparison techniques based on a pixel-by-pixel comparison are useful for many purposes, but fail to reveal important aspects of map similarities and differences. In contrast, pattern based map comparison techniques address the question of structural similarity, although with these approaches the comparison problem becomes open ended, since there is an unlimited number of ways to characteri...

Genetic algorithms for map labeling

Variational Algorithms for Marginal MAP

The marginal maximum a posteriori probability (MAP) estimation problem, which calculates the mode of the marginal posterior distribution of a subset of variables with the remaining variables marginalized, is an important inference problem in many models, such as those with hidden variables or uncertain parameters. Unfortunately, marginal MAP can be NP-hard even on trees, and has attracted less ...