Special Issue "Algorithms for Sequence Analysis and Storage"


A special issue of Algorithms (ISSN 1999-4893).

Deadline for manuscript submissions: closed (15 March 2013)

Special Issue Editor

Guest Editor
Prof. Dr. Veli Mäkinen
Department of Computer Science, University of Helsinki, P.O. Box 68, FI-00014 Helsinki, Finland
Website: http://www.cs.helsinki.fi/u/vmakinen/
E-Mail: vmakinen@cs.helsinki.fi
Interests: algorithms and data structures; computational molecular biology; sequence analysis; string algorithms; data compression; algorithm engineering

Special Issue Information

Dear Colleagues,

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
Guest Editor


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.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


  • high-throughput sequencing
  • compressed data structures
  • parallel computation
  • sequence alignment
  • fragment assembly
  • genomics
  • transcriptomics
  • metagenomics
  • epigenomics

Published Papers (7 papers)

Algorithms 2014, 7(1), 186-187; doi:10.3390/a7010186
Received: 14 March 2014; in revised form: 19 March 2014 / Accepted: 19 March 2014 / Published: 25 March 2014
Show/Hide Abstract | PDF Full-text (71 KB)

by  and
Algorithms 2014, 7(1), 62-144; doi:10.3390/a7010062
Received: 19 March 2013; in revised form: 6 February 2014 / Accepted: 14 February 2014 / Published: 7 March 2014
Show/Hide Abstract | PDF Full-text (613 KB)

by ,  and
Algorithms 2013, 6(4), 636-677; doi:10.3390/a6040636
Received: 11 June 2013; in revised form: 30 September 2013 / Accepted: 1 October 2013 / Published: 14 October 2013
Show/Hide Abstract | PDF Full-text (479 KB)

by , , , ,  and
Algorithms 2013, 6(3), 430-441; doi:10.3390/a6030430
Received: 18 March 2013; in revised form: 18 July 2013 / Accepted: 23 July 2013 / Published: 30 July 2013
Show/Hide Abstract | Cited by 1 | PDF Full-text (165 KB)

by  and
Algorithms 2013, 6(2), 352-370; doi:10.3390/a6020352
Received: 29 March 2013; in revised form: 30 April 2013 / Accepted: 3 May 2013 / Published: 22 May 2013
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by ,  and
Algorithms 2013, 6(2), 319-351; doi:10.3390/a6020319
Received: 18 March 2013; in revised form: 24 April 2013 / Accepted: 26 April 2013 / Published: 21 May 2013
Show/Hide Abstract | PDF Full-text (560 KB)

by  and
Algorithms 2013, 6(2), 309-318; doi:10.3390/a6020309
Received: 18 March 2013; in revised form: 23 April 2013 / Accepted: 27 April 2013 / Published: 21 May 2013
Show/Hide Abstract | PDF Full-text (288 KB)

Last update: 6 May 2014

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