A Fast and Specific Alignment Method for Minisatellite Maps

A Fast and Specific Alignment Method for Minisatellite Maps

BACKGROUND Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects ...

Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach

In addition to the well-known edit operations, the alignment of minisatellite maps includes duplication events. We model these duplications using a special kind of spanning trees and deduce an optimal duplication scenario by computing the respective minimum spanning tree. Based on best duplication scenarios for all substrings of the given sequences, we compute an optimal alignment of two minisa...

gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences

Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...

A Spectral Method for Fast Protein Structure Alignment

A Fast Method for Linear Space Pairwise Sequence Alignment

Pairwise sequence alignment is an important technique for finding the optimal arrangement between two sequences. A basic dynamic-programming strategy for sequence alignment needs O(mn) time and also O(mn) space. Hirschberg’s divide-and-conquer method reduces the required space to roughly 2m (m ≤ n), but it also doubles the computing time. On the other hand, the FastLSA approach adds extra rows ...