English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Adaptive seeds tame genomic sequence comparison

Kielbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011). Adaptive seeds tame genomic sequence comparison. Genome Res, 21(3), 487-93. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21209072 http://genome.cshlp.org/content/21/3/487.full.pdf.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7908-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7909-3
Genre: Journal Article

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Kielbasa, S. M.1, Author              
Wan, R., Author
Sato, K., Author
Horton, P., Author
Frith, M. C., Author
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

Content

show
hide
Free keywords: Algorithms; Base Sequence; Computational Biology/*methods; DNA/chemistry; Genome; Molecular Sequence Data; Sequence Alignment/*methods; Sequence Analysis, DNA/*methods; Software
 Abstract: The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.

Details

show
hide
Language(s):
 Dates: 2011
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Genome Res
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 21 (3) Sequence Number: - Start / End Page: 487 - 93 Identifier: ISSN: 1549-5469 (Electronic) 1088-9051 (Linking)