AVID swMATH ID: 17110 Software Authors: Bray, N., Dubchak, I., Pachter, L. Description: AVID: A Global Alignment Program. In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper. Homepage: http://genome.cshlp.org/content/13/1/97.short Related Software: BLAT; BLASTZ; MUMMER; LAGAN; ClustalW; DIALIGN; PatternHunter; MUSCLE; MAFFT; PipMaker; CLUSTAL; PHYLIP; MrBayes; Cgaln; JBROWSE; InterProScan; MAKER; EasyGene; PCAP; FragGeneScan Cited in: 9 Publications all top 5 Cited by 20 Authors 1 Axelson-Fisk, Marina 1 Cho, Hwan-Gue 1 Choi, Jeong-Hyeon 1 Coull, Scott E. 1 Gibney, Daniel 1 Guo, Xuan 1 Jain, Chirag 1 Keith, Jonathan M. 1 Lemaitre, Claire 1 Măndoiu, Ion I. 1 Nguyen, Ken 1 Pan, Yi 1 Sagot, Marie-France 1 Shasha, Dennis E. 1 Szymanski, Boleslaw K. 1 Thankachan, Sharma V. 1 Toivonen, Hannu T. T. 1 Wang, Jason Tsong Li 1 Zaki, Mohammed Javeed 1 Zelikovsky, Alexander Z. all top 5 Cited in 6 Serials 1 Theoretical Computer Science 1 Computational Statistics and Data Analysis 1 Computational Biology and Chemistry 1 Computational Biology 1 Methods in Molecular Biology 1 Advanced Information and Knowledge Processing all top 5 Cited in 6 Fields 8 Biology and other natural sciences (92-XX) 2 General and overarching topics; collections (00-XX) 2 Statistics (62-XX) 2 Computer science (68-XX) 1 Probability theory and stochastic processes (60-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year