BLAT--the BLAST-like alignment tool.

By W. James Kent. Genome Research, 2002

8,949 citations recorded by the source corpus.

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-based BLAT server for the human genome.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2878976835c73ed0906e17a7336b9bf10d491a1a

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Ultrafast clustering algorithms for metagenomic sequence analysis (2012, methodology): “DATABASE SEARCH In metagenomic projects, an important annotation step is to query the reads or Open Reading Frames (ORF) against reference databases of known genomes, DNAs or proteins with an alignment program such as basic local alignment search tool (BLAST) [27], BWA [65], BLAT [66], FR-HIT [67] o”
High-resolution mapping and characterization of open chromatin across the genome. (2008, methodology): “and Characterization of Open Chromatin across the Genome”
Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology (2009, methodology): “To increase the number of SNPs mapped to a specific position within the genome, the flanking sequences for all 64,232 SNPs were aligned to the new build using BLAT [19].”
Draft genome of the living fossil Ginkgo biloba (2016, methodology): “Assembled transcripts and retrieved ESTs were mapped to the ginkgo genome using blat [72] (V34) with default parameters and the sim4 output format.”
Fast model-based protein homology detection without alignment (2007, methodology): “, 2004a, b)—the mismatch-kernel is similar to the BLAT alignment (Kent, 2002), (f) the SVMpairwise (Liao and Noble, 2002)—feature vector is the SwithWaterman alignment score to all other training sequences, (g) SW-kernel (Vert et al.”
A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms (2007, methodology): “The performances of BLAST, BLAT, and mega-BLAST were very similar in most cases with most of the variation occurring between, rather than among, data sets (Tables 2 and 3).”
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools (2012, methodology): “Replacing the algorithms used to perform similarity searches (most commonly BLAST [6]) with more efficient algorithms like BLAT[7] will provide a much needed reduction in analysis cost.”
A Map of Recent Positive Selection in the Human Genome (2006, methodology): “To obtain ancestral states for all SNPs, we obtained FASTA sequences for each SNP as specified for that rs entry in the dbSNP database, and aligned those to the draft genome build of the chimp sequence, obtained from the UCSC database [12] using blat, version 27 [48].”