Skip Navigation


Bioinformatics Advance Access originally published online on February 12, 2004
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/9/1459    most recent
bth083v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (3)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Schmollinger, M.
Right arrow Articles by Zell, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schmollinger, M.
Right arrow Articles by Zell, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

Applications Note

ParSeq: searching motifs with structural and biochemical properties

M. Schmollinger *, I. Fischer , C. Nerz , S. Pinkenburg , F. Götz , M. Kaufmann , K.-J. Lange , R. Reuter , W. Rosenstiel and A. Zell

Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany

Received on October 7, 2003; accepted on December 16, 2003
Advance Access Publication February 12, 2004

Summary: Searches for variable motifs such as protein-binding sites or promoter regions are more complex than the search for casual motifs. For example, in amino acid sequences comparing motifs alone mostly proves to be insufficient to detect regions that represent proteins with a special function, because the function depends on biochemical properties of individual amino acids (such as polarity or hydrophobicity). Pure string matching programs are not able to find these motifs; hence, we developed ParSeq, a program that combines the search for motifs with certain structural properties, the verification of biochemical properties, an approximate search mechanism and a stepwise creation of the motif description by allowing to search on previously obtained results.

Availability: http://www-pr.informatik.uni-tuebingen.de/parseq

Contact: parseq{at}informatik.uni-tuebingen.de

* To whom correspondence should be addressed.


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
L. Biswas, R. Biswas, C. Nerz, K. Ohlsen, M. Schlag, T. Schafer, T. Lamkemeyer, A.-K. Ziebandt, K. Hantke, R. Rosenstein, et al.
Role of the Twin-Arginine Translocation Pathway in Staphylococcus
J. Bacteriol., October 1, 2009; 191(19): 5921 - 5929.
[Abstract] [Full Text] [PDF]

Home page
 Infect. Immun.Home page
H. Stoll, J. Dengjel, C. Nerz, and F. Gotz
Staphylococcus aureus Deficient in Lipidation of Prelipoproteins Is Attenuated in Growth and Immune Activation
Infect. Immun., April 1, 2005; 73(4): 2411 - 2423.
[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.