BLAT

BLAT — The BLAST-Like Alignment Tool. Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT’s speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be homologous to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-basedBLAT server for the human genome.


References in zbMATH (referenced in 34 articles )

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  1. Retzlaff, Nancy; Stadler, Peter F.: Partially local multi-way alignments (2018)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  4. Kim, Jongkyu; Reinert, Knut: Vaquita: fast and accurate identification of structural variation using combined evidence (2017)
  5. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  6. Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)
  7. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  8. Kotsifakos, Alexios; Stefan, Alexandra; Athitsos, Vassilis; Das, Gautam; Papapetrou, Panagiotis: DRESS: dimensionality reduction for efficient sequence search (2015)
  9. O’Donnell, Brian; Maurer, Alexander; Papandreou-Suppappola, Antonia: Biosequence time-frequency processing: pathogen detection and identification (2015)
  10. Egidi, Lavinia; Manzini, Giovanni: Better spaced seeds using quadratic residues (2013)
  11. Policriti, Alberto; Tomescu, Alexandru I.; Vezzi, Francesco: A randomized numerical aligner (rNA) (2012)
  12. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  13. Wilke, Andreas; Wilkening, Jared; Glass, Elizabeth M.; Desai, Narayan L.; Meyer, Folker: An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud (2011) ioport
  14. Churbanov, Alexander G.; Vorechovsky, Igor; Hicks, Chindo: A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements (2010) ioport
  15. De Schrijver, Joachim M.; De Leeneer, Kim; Lefever, Steve; Sabbe, Nick; Pattyn, Filip; Van Nieuwerburgh, Filip; Coucke, Paul; Deforce, Dieter; Vandesompele, Jo; Bekaert, Sofie; Hellemans, Jan; Van Criekinge, Wim: Analysing 454 amplicon resequencing experiments using the modular and database oriented variant identification pipeline (2010) ioport
  16. Homer, Nils; Nelson, Stanley F.; Merriman, Barry: Local alignment of generalized k-base encoded DNA sequence (2010) ioport
  17. Kolbe, Dashiell; Zhu, Qiang; Pramanik, Sakti: Reducing non-determinism of (k)-NN searching in non-ordered discrete data spaces (2010)
  18. Nakato, Ryuichiro; Gotoh, Osamu: Cgaln: fast and space-efficient whole-genome alignment (2010) ioport
  19. Palmer, Lance E.; Dejori, Mathäus; Bolanos, Randall A.; Fasulo, Daniel P.: Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction (2010) ioport
  20. Wu, Jing: Testing the coding potential of conserved short genomic sequences (2010) ioport

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