Buy this book
The meaning of biological sequences is a central problem of modern biology. Although string matching is well understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. To align biologically reasonable strings, we proposed the Walking Tree Method, an approximate string alignment method that can handle insertion, deletions, substitutions, translocations, and more than one level of inversions. Our earlier versions were able to align whole bacterial genomes (approx.1 Mbps) and discover and verify genes. As extremely long sequences can now be deciphered rapidly and accurately without amplification, speeding up the method becomes necessary. Via a technique that we call it "recurrence reduction" in which same computations can be looked up rather than recomputed, we are able to significantly improve the performance, e.g., 400% for 1-million base pair alignments.
Buy this book
Showing 1 featured edition. View all 1 editions?
Edition | Availability |
---|---|
1
Fast walking tree method via recurrence reduction for biological string alignment
2002, Oregon State University, Dept. of Computer Science
in English
|
aaaa
|
Book Details
Published in
[Corvallis, OR
Edition Notes
Caption title.
"May 2002."
Includes bibliographical references (leaves [6]-[7]).
Also available on the World Wide Web.
The Physical Object
ID Numbers
Community Reviews (0)
Feedback?January 21, 2010 | Edited by WorkBot | add subjects and covers |
December 11, 2009 | Created by WorkBot | add works page |