English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Syntenator: Multiple gene order alignments with a gene-specific scoring function

Rödelsperger, C., & Dieterich, C. (2008). Syntenator: Multiple gene order alignments with a gene-specific scoring function. Algorythms for Molecular Biology, 3, 14-14. doi:10.1186/1748-7188-3-14.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7EB6-4 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7EB7-2
Genre: Journal Article

Files

show Files
hide Files
:
1748-7188-3-14.pdf (Any fulltext), 404KB
Name:
1748-7188-3-14.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
eDoc_access: PUBLIC
License:
-

Locators

show

Creators

show
hide
 Creators:
Rödelsperger, Christian1, Author              
Dieterich, Christoph2, Author
Affiliations:
1Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433557              
2Max Planck Society, ou_persistent13              

Content

show
hide
Free keywords: -
 Abstract: Background Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case of conserved syntenies, such regions are defined as conserved gene orders. On the gene order level, homologous regions can even be found between distantly related genomes, which do not align on the nucleotide sequence level. Results We present a novel approach to identify regions of conserved synteny across multiple genomes. Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations. Conclusion We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from http://www2.tuebingen.mpg.de/abt4/plone webcite.

Details

show
hide
Language(s): eng - English
 Dates: 2008-11-06
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Algorythms for Molecular Biology
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 3 Sequence Number: - Start / End Page: 14 - 14 Identifier: ISSN: 1748-7188