Comparing Degenerate Strings

A Text Transformation Scheme for Degenerate Strings

The Burrows-Wheeler Transformation computes a permutation of a string of letters over an alphabet, and is well-suited to compression-related applications due to its invertability and data clustering properties. For space e ciency the input to the transform can be preprocessed into Lyndon factors. We consider scenarios with uncertainty regarding the data: a position in an indeterminate or degene...

Efficient Pattern Matching in Elastic-Degenerate Strings

In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such that each elastic-degenerate symbol corresponds to a set of two or more variable length strings. Here, we present an algorithm for solving the pattern matchi...

The Constrained Longest Common Subsequence Problem for Degenerate Strings

Using an alignment of fragment strings for comparing protein structures

MOTIVATION Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can be a powerful tool for protein structure comparison and classification, given the arsenal of sequence compa...

Describing and comparing protein structures using shape strings.

Different methods for describing and comparing the structures of the tens of thousands of proteins that have been determined by X-ray crystallography are reviewed. Such comparisons are important for understanding the structures and functions of proteins and facilitating structure prediction, as well as assessing structure prediction methods. We summarize methods in this field emphasizing ways o...