English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach.

Schliep, A., & Krause, R. (2007). Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach. In S. H. Raffaele Giancarlo (Ed.), Algorithms in Bioinformatics (pp. 383-394). Berlin / Heidelberg: Springer.

Item is

Files

show Files
hide Files
:
fulltext.pdf (Any fulltext), 2MB
 
File Permalink:
-
Name:
fulltext.pdf
Description:
-
OA-Status:
Visibility:
Restricted (Max Planck Institute for Molecular Genetics, MBMG; )
MIME-Type / Checksum:
application/pdf
Technical Metadata:
Copyright Date:
-
Copyright Info:
eDoc_access: MPG
License:
-

Locators

show

Creators

show
hide
 Creators:
Schliep, Alexander1, Author           
Krause, Roland1, Author           
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

Content

show
hide
Free keywords: -
 Abstract: Genomic tiling arrays are a type of DNA microarrays which can investigate the complete genome of arbitrary species for which the sequence is known. The design or selection of suitable oligonucleotide probes for such arrays is however computationally difficult if features such as oligonucleotide quality and repetitive regions are to be considered. We formulate the minimal cost tiling path problem for the selection of oligonucleotides from a set of candidates, which is equivalent to a shortest path problem. An efficient implementation of Dijkstra’s shortest path algorithm allows us to compute globally optimal tiling paths from millions of candidate oligonucleotides on a standard desktop computer. The solution to this multi-criterion optimization is spatially adaptive to the problem instance. Our formulation incorporates experimental constraints with respect to specific regions of interest and tradeoffs between hybridization parameters, probe quality and tiling density easily. Solutions for the basic formulation can be obtained more efficiently from Monge theory.

Details

show
hide
Language(s): eng - English
 Dates: 2007
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Algorithms in Bioinformatics
Source Genre: Book
 Creator(s):
Raffaele Giancarlo, Sridhar Hannenhalli, Editor
Affiliations:
-
Publ. Info: Berlin / Heidelberg : Springer
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 383 - 394 Identifier: ISBN: 978-3-540-74125-1

Source 2

show
hide
Title: Lecture Notes in Computer Science
Source Genre: Series
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 4645 Sequence Number: - Start / End Page: - Identifier: -