Sequence alignment as a method for human activity analysis in space and time

Noam Shoval*, Michal Isaacson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

187 Scopus citations


This article introduces the method of sequence alignment as a tool for analyzing the sequential aspects within the temporal and spatial dimensions of human activities. Sequence alignment was first developed during the 1980s and employed by biochemists to analyze DNA sequences. Toward the end of the 1990s it was adapted for use in the social sciences. However, unlike other social sciences practitioners, geographers have not, until now, exploited this method. In contrast to traditional quantitative methods, sequence alignment, as its name suggests, is directly concerned with the order (sequence) of events, and is therefore well suited for the pursuit of time-geographic research. To demonstrate the merits of sequence alignment for geographic research, a database composed of forty space-time sequences of visitors who had visited the Old City of Akko (Israel) was used. The sequences were obtained by means of GPS devices, which were distributed among the visitors tracked and which they operated for the duration of their visit to the city. The sequences thereby obtained were aligned using ClustalG, a sequence alignment computer program. The result of this analysis was the identification of three temporal-spatial time geographies of the visitors that were sampled in this study.

Original languageAmerican English
Pages (from-to)282-297
Number of pages16
JournalAnnals of the Association of American Geographers
Issue number2
StatePublished - Jun 2007

Bibliographical note

Funding Information:
This research was supported by The Israel Science Foundation (grant No. 832/03). We thank Clarke Wilson for guiding us through the complexities of the ClustalG program; Bertine Bargeman and Harry Timmermans for sharing their ideas on sequence alignment methods with the first author during a Ph.D. workshop held in Eindhoven, The Netherlands (20–23 October 1999); The Old Akko Development Company Ltd. for their assistance to the field work; Tamar Soffer for drawing the maps and diagrams; Adi Bennun for his constructive advice on GIS visualization; Joshua Rosenbloom for his comments on the manuscript; and four anonymous reviewers and the section editor for comments on earlier versions of this article.

Funding Information:
Sankoff and Kruskal’s algorithms and their various offshoots led to the development of a number of sequence alignment computer programs. As the majority of these programs were developed for use in biochemistry, their alphabet was limited to the twenty characters needed to denote the amino acids, but analysis of socioeconomic data requires a much larger alphabet. An expanded alphabet, by representing as wide a range as possible of human activities (or in our case, geographic locations), allows researchers to tailor programs in accordance with their specific needs. Several computer programs have been either written specifically for the social sciences or adapted from existing biochemistry programs. For this study we used the ClustalG program, a general version of the ClustalX sequence alignment program used to analyze protein and nucleotide molecules. The ClustalG program was adapted for general use by Andrew Harvey of the Department of Economics, St. Mary’s University, Halifax; Julie Thompson of the In-stitut de Génétique et de Biologie Moléculaire et Cel-lulaire, Strasbourg; and Clarke Wilson of the Canada Mortgage and Housing Corporation. The Social Sciences and Humanities Research Council of Canada funded the project as part of its Activity Settings, Sequencing, and Measurement of Time Allocation Patterns project (1998).


  • Clustal G
  • Global positioning systems (GPS)
  • Sequence alignment
  • Time geography


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