BLAT statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

BLAT specifications

Information


Unique identifier OMICS_01434
Name BLAT
Alternative name BLAST-Like Alignment Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • pslReps

Versioning


No version available

Maintainer


  • person_outline bigWig format Team

Information


Unique identifier OMICS_01434
Name BLAT
Alternative name BLAST-Like Alignment Tool
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • pslReps

Maintainer


  • person_outline bigWig format Team

Publications for BLAST-Like Alignment Tool

BLAT citations

 (1932)
library_books

Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes

2018
Sci Rep
PMCID: 5935709
PMID: 29728663
DOI: 10.1038/s41598-018-25498-2

[…] o vs. OKF6/TERT1-Parental and OKF6/TERT1-Smoke vs. OKF6/TERT1-Parental were further investigated for differential expression using DESeq.Novel miRNAs were assessed for the genomic location using UCSC BLAT. They were also queried against database YM500V3 using ‘genomic location search’ option. YM500V3 is a repository of novel miRNA built using >8,000 smRNA data-sets pertaining to various cancers al […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] luated using available public transcript sequence tags or expressed sequence tags. Core eukaryotic genes identified by CEGMA v.2.3 (Parra et al., ) were remapped to the A. ipaensis genome assembly by BLAT (Kent, ) to evaluate the quality of the assembly. CEGMA data were downloaded from the Korf Lab research group at the Genome Center, UC Davis (http://korflab.ucdavis.edu/datasets/cegma/#SCT6). […]

library_books

Taxon Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient

2018
Front Microbiol
PMCID: 5943556
PMID: 29774016
DOI: 10.3389/fmicb.2018.00869

[…] ene contents, contigs were submitted to the MG-RAST webserver (Glass et al., ) and ORF prediction was conducted using the FragGeneScan tool (Rho et al., ). Afterwards, contigs were annotated with the BLAT tool implemented in MG-RAST against the SEED database using stringent filtering parameters (1e−12 as p-value, 85% identity as threshold, 50 base pairs as minimum alignment length). Statistical su […]

library_books

Reconstruction of a replication competent ancestral murine endogenous retrovirus L

2018
Retrovirology
PMCID: 5930517
PMID: 29716624
DOI: 10.1186/s12977-018-0416-3

[…] hat would specifically anneal to the predicted integration site, based on the previously sequenced 3′ flanking sequence. The resulting CHO gDNA sequences were mapped to the CHO genome (criGri1) using BLAT [] searches on the UCSC genome browser []. To account for biases due to location and density of EcoRV restriction sites, we compared the distribution of the 26 ancML integration sites to matched […]

library_books

The genetic architecture of floral traits in the woody plant Prunus mume

2018
Nat Commun
PMCID: 5923208
PMID: 29703940
DOI: 10.1038/s41467-018-04093-z

[…] ed after aligning all mei and Prunus genomes analyzed here during the establishment of the core- and pan-genome. Then these previously unaligned sequences were realigned to the reference genome using BLAT and unaligned sequences with identity <95% and length >100 bp were extracted. Finally, sequences generated from each assembly above were aligned to any other assemblies to identify any sequences […]

call_split

A Novel Whole Gene Deletion of BCKDHB by Alu Mediated Non allelic Recombination in a Chinese Patient With Maple Syrup Urine Disease

2018
Front Genet
PMCID: 5928131
PMID: 29740478
DOI: 10.3389/fgene.2018.00145
call_split See protocol

[…] Approximately, 5000 bp of the contig sequence from LR-PCR was analyzed to identify two breakpoints of the gross deletion with BLAT using the UCSC Genome Browser. The known repetitive elements were evaluated by CENSOR at the 300 nucleotide sequence flanking each breakpoint using the February 2009 human reference sequence (GRC […]

Citations

Looking to check out a full list of citations?

BLAT institution(s)
National Institutes of Health Library, National Institutes of Health, Bethesda, MD, USA

BLAT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BLAT