BLASTZ

Human-mouse alignments with BLASTZ. The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.


References in zbMATH (referenced in 12 articles )

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  2. Elloumi, Mourad (ed.); Zomaya, Albert Y. (ed.): Algorithms in computational molecular biology. Techniques approaches and applications. (2011)
  3. Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris: Translog, a web browser for studying the expression divergence of homologous genes (2010) ioport
  4. Nakato, Ryuichiro; Gotoh, Osamu: Cgaln: fast and space-efficient whole-genome alignment (2010) ioport
  5. Ratan, Aakrosh; Zhang, Yu; Hayes, Vanessa M.; Schuster, Stephan C.; Miller, Webb: Calling SNPs without a reference sequence (2010) ioport
  6. Swidan, Firas; Shamir, Ron: Assessing the quality of whole genome alignments in bacteria (2009) ioport
  7. Christley, Scott; Lobo, Neil F.; Madey, Greg: Multiple organism algorithm for finding ultraconserved elements (2008) ioport
  8. Hilewitz, Yedidya; Lee, Ruby B.: Fast bit gather, bit scatter and bit permutation instructions for commodity microprocessors (2008) ioport
  9. 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)
  10. Joseph, Jijoy; Sasikumar, Roschen: Chaos game representation for comparison of whole genomes (2006) ioport
  11. Abouelhoda, Mohamed Ibrahim; Ohlebusch, Enno: Chaining algorithms for multiple genome comparison (2005)
  12. Choi, Jeong-Hyeon; Cho, Hwan-Gue; Kim, Sun: GAME: A simple and efficient whole genome alignment method using maximal exact match filtering (2005)