English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  andi: fast and accurate estimation of evolutionary distances between closely related genomes

Haubold, B., Klötzl, F., & Pfaffelhuber, P. (2015). andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics, 31(8), 1169-1175. doi:10.1093/bioinformatics/btu815.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0024-9D24-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-1A13-9
Genre: Journal Article

Files

show Files
hide Files
:
Haubold_Kloetzl Pfaffelhuber_2014.pdf (Publisher version), 4MB
 
File Permalink:
-
Name:
Haubold_Kloetzl Pfaffelhuber_2014.pdf
Description:
-
Visibility:
Restricted (Max Planck Institute for Evolutionary Biology, Plön; )
MIME-Type / Checksum:
application/pdf
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Locators

show

Creators

show
hide
 Creators:
Haubold, Bernhard1, Author              
Klötzl, Fabian1, Author              
Pfaffelhuber, Peter, Author
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

Content

show
hide
Free keywords: -
 Abstract: Motivation: A standard approach to classifying sets of genomes is to calculate their pairwise distances. This is difficult for large samples. We have therefore developed an algorithm for rapidly computing the evolutionary distances between closely related genomes. Results: Our distance measure is based on ungapped local alignments that we anchor through pairs of maximal unique matches of a minimum length. These exact matches can be looked up efficiently using enhanced suffix arrays and our implementation requires approximately only 1 s and 45 MB RAM/Mbase analysed. The pairing of matches distinguishes non-homologous from homologous regions leading to accurate distance estimation. We show this by analysing simulated data and genome samples ranging from 29 Escherichia coli/Shigella genomes to 3085 genomes of Streptococcus pneumoniae. Availability and implementation: We have implemented the computation of anchor distances in the multithreaded UNIX command-line program andi for ANchor DIstances. C sources and documentation are posted at http://github.com/evolbioinf/andi/ Contact: haubold@evolbio.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Details

show
hide
Language(s): eng - English
 Dates: 2014-11-062014-07-012014-12-072014-12-102015-04-15
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1093/bioinformatics/btu815
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Bioinformatics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 31 (8) Sequence Number: - Start / End Page: 1169 - 1175 Identifier: ISSN: 1367-4803 (print)
ISSN: 1460-2059 (online)
CoNE: /journals/resource/954926969991