Skip Navigation



Bioinformatics Advance Access published online on October 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti091
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/7/853    most recent
bti091v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bartels, D.
Right arrow Articles by Schuster, S. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bartels, D.
Right arrow Articles by Schuster, S. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received July 22, 2004
Revised September 16, 2004
Accepted October 7, 2004

Article

BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

Daniela Bartels 1, Sebastian Kespohl 1, Stefan Albaum 1, Tanja Drüke 1, Alexander Goesmann 1, Julia Herold 1, Olaf Kaiser 2, Alfred Pühler 2, Friedhelm Pfeiffer 3, Günter Raddatz 4, Jens Stoye 5, Folker Meyer 1*, and Stephan C. Schuster 4

1 Universität Bielefeld, Center for Biotechnology (CeBiTec), D-33594 Bielefeld, Germany
2 Universität Bielefeld, Lehrstuhl für Genetik, Fakultät für Biologie, D-33594 Bielefeld, Germany
3 Max-Planck-Institut für Biochemie, Abt. Membranbiochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany
4 Max-Planck-Institut für Entwicklungsbiologie, Spemannstr. 35, D-72076 Tübingen, Germany
5 Universität Bielefeld, Technische Fakultät, D-33594 Bielefeld, Germany

* To whom correspondence should be addressed.
Folker Meyer, E-mail: fm{at}Cebitec.Uni-Bielefeld.DE


  Abstract

Motivation: Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

Summary: We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages.

Availability: The BACCardI tool is freely available at http://www.cebitec.uni-bielefeld.de/groups/brf/software/baccardi/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Bacteriol.Home page
K.-H. Gartemann, B. Abt, T. Bekel, A. Burger, J. Engemann, M. Flugel, L. Gaigalat, A. Goesmann, I. Grafen, J. Kalinowski, et al.
The Genome Sequence of the Tomato-Pathogenic Actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 Reveals a Large Island Involved in Pathogenicity
J. Bacteriol., March 15, 2008; 190(6): 2138 - 2149.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J.-H. Choi, S. Kim, H. Tang, J. Andrews, D. G. Gilbert, and J. K. Colbourne
A machine-learning approach to combined evidence validation of genome assemblies
Bioinformatics, March 15, 2008; 24(6): 744 - 750.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. C. Richter, S. C. Schuster, and D. H. Huson
OSLay: optimal syntenic layout of unfinished assemblies
Bioinformatics, July 1, 2007; 23(13): 1573 - 1579.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Buttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, et al.
Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence
J. Bacteriol., November 1, 2005; 187(21): 7254 - 7266.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.