LAGAN

The Lagan Tookit is a set of alignment programs for comparative genomics. The three main components are a pairwise aligner (LAGAN), a multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy. The results of the alignment can be visualized using the VISTA visualization tool.


References in zbMATH (referenced in 17 articles )

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  1. Wu, Chengyuan; Ren, Shiquan; Wu, Jie; Xia, Kelin: Magnus representation of genome sequences (2019)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  3. Erciyes, K.: Distributed and sequential algorithms for bioinformatics (2015)
  4. Federico, Maria; Peterlongo, Pierre; Pisanti, Nadia; Sagot, Marie-France: \textscRime: repeat identification (2014)
  5. Giancarlo, R.; Scaturro, D.; Utro, F.: Textual data compression in computational biology: algorithmic techniques (2012)
  6. Kim, Jaebum; Sinha, Saurabh: Towards realistic benchmarks for multiple alignments of non-coding sequences (2010) ioport
  7. Kryukov, Kirill; Saitou, Naruya: MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data (2010) ioport
  8. Nakato, Ryuichiro; Gotoh, Osamu: Cgaln: fast and space-efficient whole-genome alignment (2010) ioport
  9. Iliopoulos, Costas S.; Rahman, M. Sohel: Indexing factors with gaps (2009)
  10. Nguyen, Tung T.; Androulakis, Ioannis P.: Recent advances in the computational discovery of transcription factor binding sites (2009)
  11. Christley, Scott; Lobo, Neil F.; Madey, Greg: Multiple organism algorithm for finding ultraconserved elements (2008) ioport
  12. Doring, Andreas; Weese, David; Rausch, Tobias; Reinert, Knut: Seqan - an efficient, generic C++ library for sequence analysis (2008) ioport
  13. Lemaitre, Claire; Sagot, Marie-France: A small trip in the untranquil world of genomes: a survey on the detection and analysis of genome rearrangement breakpoints (2008)
  14. Schatz, Michael C.; Trapnell, Cole; Delcher, Arthur L.; Varshney, Amitabh: High-throughput sequence alignment using graphics processing units (2007) ioport
  15. Wang, Adrienne X.; Ruzzo, Walter L.; Tompa, Martin: How accurately is ncrna aligned within whole-genome multiple alignments? (2007) ioport
  16. Abouelhoda, Mohamed Ibrahim; Ohlebusch, Enno: Chaining algorithms for multiple genome comparison (2005)
  17. Choi, Jeong-Hyeon; Cho, Hwan-Gue; Kim, Sun: GAME: A simple and efficient whole genome alignment method using maximal exact match filtering (2005)