Dynamic edit distance table under a general weighted cost function

Dynamic Edit Distance Table under a General Weighted Cost Function

Approximate String Searching under Weighted Edit Distance

Let p 2 be a string of length m and t 2 be a string of length n. The approximate string searching problem is to nd all approximate matches of p in t having weighted edit distance at most k from p. We present a new method that preprocesses the pattern into a DFA which scans t online in linear time, thereby recognizing all positions in t where an approximate match ends. We show how to reduce the ...

Edit-Distance Of Weighted Automata: General Definitions And Algorithms

The problem of computing the similarity between two sequences arises in many areas such as computational biology and natural language processing. A common measure of the similarity of two strings is their edit-distance, that is the minimal cost of a series of symbol insertions, deletions, or substitutions transforming one string into the other. In several applications such as speech recognition...

A General Edit Distance between RNA Structures

Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of nested arcs and a set of crossing arcs, respectively. Since RNA functions are largely determined by molecular confirmation and therefore secondary and tertiary structures, the comparison between RNA secondary and tertiar...

Dynamic Programming: Minimum Edit Distance

with 3 edits (delete the C, delete the last A and insert a C). This is the best that can be done so the minimum edit distance is 3. The MED problem is an important problem that has many applications. For example in version control systems such as git or svn when you update a file and commit it, the system does not store the new version but instead only stores the “difference” from the previous ...