Special Issue "Algorithms for Sequence Analysis and Storage"
A special issue of Algorithms (ISSN 1999-4893).
Deadline for manuscript submissions: closed (15 March 2013)
Prof. Dr. Veli Mäkinen
Department of Computer Science, University of Helsinki, P.O. Box 68, FI-00014 Helsinki, Finland
Interests: algorithms and data structures; computational molecular biology; sequence analysis; string algorithms; data compression; algorithm engineering
Analysis of high-throughput sequencing data has become a crucial component in genome research. For example, methods based on latest developments in compressed data structures, namely index structures exploiting Burrows-Wheeler transform, are widely deployed in the discovery of disease causing mutations. The success of such approaches is due to being able to solve the dilemma of the indexing requiring more space than the data itself, where the data itself is enormous. Also parallel computation and use of special hardware like GPUs have shown to be important paradigms to provide scalable analysis methods. With our already increased knowledge about the genomic structure of the whole human population, and with the development of sequencing techniques and their applications in studying RNAs, metapopulations, and epigenetics, the field seeks for new innovative and universal algorithmic approaches that scale for current and future needs in the analysis and storage of biological sequences. This special issue is dedicated to approaches to biological sequence analysis that have algorithmic novelty and potential for fu ndamental impact in methods used for genome research. Also theoretical studies increasing our understanding on the limits of indexing, compression, and parallel computation in this context are welcome.
Prof. Dr. Veli Mäkinen
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Algorithms is an international peer-reviewed Open Access quarterly journal published by MDPI.
- high-throughput sequencing
- compressed data structures
- parallel computation
- sequence alignment
- fragment assembly
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Authors: Enno Ohlebusch, Katharina Berger and Timo Beller
Affiliation: Institute of Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany
Title: Space-Efficient Computation of Maximal and Supermaximal Repeats in Genome Sequences
Abstract: The identification of repetitive sequences (repeats) is an essential component of genome sequence analysis, and the notions of maximal and supermaximal repeats capture all exact repeats in a genome in a compact way. Very recently, Külekci et al. (Computational Biology and Bioinformatics, 2012) developed an algorithm for finding all maximal repeats that is very space-efficient because it uses the Burrows-Wheeler transform and wavelet trees. In this paper, we present a new space-efficient algorithm for finding maximal repeats in massive data that outperforms their algorithm both in theory and practice. The algorithm is not confined to this task, it can also be used to find all supermaximal repeats or to solve other problems space-efficiently.
Last update: 14 November 2012