Summary
The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a “glocal” alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.
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Acknowledgments
Many people have contributed to the development of the LAGAN Toolkit during its development. Michael F. Kim and Chuong B. Do were actively involved in the original development, including writing many of the utilities. Sanket Malde and Mukund Sundararajan developed the 1-monotonic chaining algorithm, and Serafim Batzoglou supervised the development of the software (and the degrees of the people writing it).
Our early users bore the brunt of the bugs in the package, with Kerrin Small and Gregory M. Cooper (working with Arend Sidow) deserving special recognition for being the first to use the programs on their own. Alexander Poliakov and Inna Dubchak were the first to use LAGAN in a large scale pipeline and hence also helped identify several problems with the software. This manuscript is partially based on the original Lagan and CHAOS papers as well as on a book chapter appearing in the Handbook of Computational Biology (S. Aluru, ed). The author's research was funded by the NSF Graduate Fellowship Award and the NSERC Discovery Grant during the writing.
Finally, I would like to thank the many users of LAGAN (both standalone and through the website) who have made this into a popular alignment package while also keeping the developers appraised of the problems and being patient as the problems were fixed.
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Brudno, M. (2007). An Introduction to the Lagan Alignment Toolkit. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_13
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DOI: https://doi.org/10.1007/978-1-59745-514-5_13
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