Name
Title | ||
|---|---|---|
Fast Structural Alignment Of Biomolecules Using A Hash Table, N-Grams And String Descriptors |
Abstract | ||
|---|---|---|
This work presents a generalized approach for the fast structural alignment of thousands of macromolecular structures. The method uses string representations of a macromolecular structure and a hash table that stores n-grams of a certain size for searching. To this end, macromolecular structure-to-string translators were implemented for protein and RNA structures. A query against the index is performed in two hierarchical steps to unite speed and precision. In the first step the query structure is translated into n-grams, and all target structures containing these n-grams are retrieved from the hash table. In the second step all corresponding n-grams of the query and each target structure are subsequently aligned, and after each alignment a score is calculated based on the matching n-grams of query and target. The extendable framework enables the user to query and structurally align thousands of protein and RNA structures on a commodity machine and is available as open source from http://lajolla.sf.net. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.3390/a2020692 | ALGORITHMS |
Keywords | Field | DocType |
Structural alignment, protein, RNA, hash table, n-gram, torsion angles | Structural alignment,Computer science,Rolling hash,Theoretical computer science,n-gram,Hash function,Macro,Hash table | Journal |
Volume | Issue | Citations |
2 | 2 | 16 |
PageRank | References | Authors |
0.80 | 19 | 7 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Raphael André Bauer | 1 | 32 | 1.87 |
| Kristian Rother | 2 | 215 | 24.71 |
| Peter Moor | 3 | 16 | 0.80 |
| Knut Reinert | 4 | 1020 | 105.87 |
| Thomas Steinke | 5 | 178 | 15.49 |
| Janusz M. Bujnicki | 6 | 352 | 33.92 |
| Robert Preissner | 7 | 695 | 49.17 |