Skip Navigation



Bioinformatics Advance Access published online on March 17, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti393
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary data
Right arrow All Versions of this Article:
21/11/2573    most recent
bti393v1
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 Kivioja, T.
Right arrow Articles by Ukkonen, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kivioja, T.
Right arrow Articles by Ukkonen, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received September 21, 2004
Revised March 14, 2005
Accepted March 15, 2005

Article

Optimization of cDNA-AFLP experiments using genomic sequence data

Teemu Kivioja 1*, Mikko Arvas 2, Markku Saloheimo 2, Merja Penttilä 2, and Esko Ukkonen 1

1 Department of Computer Science, University of Helsinki, Helsinki, P.O. Box 68, FIN-00014, Finland
2 VTT Biotechnology, Espoo, P.O. Box 1500, FIN-02044, Finland

* To whom correspondence should be addressed.
Teemu Kivioja, E-mail: Teemu.Kivioja{at}vtt.fi


  Abstract

Motivation: cDNA-AFLP is one of the few genome-wide level expression profiling methods capable of finding genes that have not been cloned or even predicted from sequence before but have interesting expression patterns under the studied conditions. In cDNA-AFLP a complex cDNA mixture is divided into small subsets using restriction enzymes and selective PCR. A large cDNA-AFLP experiment can require a substantial amount of resources such as hundreds of PCR amplifications and gel electrophoresis runs followed by manual cutting of a large number of bands from the gels. Our aim was to test whether this workload can be reduced by rational design of the experiment.

Results: We used the available genomic sequence information to optimize cDNA-AFLP experiments beforehand so that as many transcripts as possible could be profiled with a given amount of resources. Optimization of the selection of both restriction enzymes and selective primers for cDNA-AFLP experiments has not been done before. The in silico tests performed suggest that substantial amounts of resources can be saved by optimization of cDNA-AFLP experiments.

Availability: A Perl implementation of the optimization method is available upon request from the authors.


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




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.