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

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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 <>

BLAT articles

BLAT citations

 (59)
2018
PMCID: 5884551

[…] 0.9—outfiltermultimapnmax 1) against the public genome (bioproject: prjna72441) that we had annotated before by aligning the above-mentioned naked mole-rat transcriptome reference using blat [94] and splign [95]. rat reads were aligned against the mentioned refseq reference using bwa aln [96] (-n 2 -o 0 -e 0 -o 1000 -e 1000). read data and counts were deposited as geo (gene […]

2018
PMCID: 5791963

[…] compared to those reported previously [18,22]. newly identified genes were confirmed using blast search of dog genomic sequences (available at ncbi.nlm.nih.gov/projects/mapview, [33]) and/or dog blat search (available at genome.ucsc.edu, [34]), using the canfam3.1 assembly (genbank assembly id gca_000002285.2)., for cll cases, genomic dna was extracted from 200 μl peripheral whole blood […]

2017
PMCID: 5767953

[…] and multiz. the resulting 583 regions, 6,126 bp long on an average, were termed hcondels, 510 of which were later confirmed by mclean et al. (2011) by direct alignment with a human sequence, using blat (kent 2002). interestingly, 88% of these human deletions were also discovered in the neanderthal, indicating that the majority of hcondels occurred before human-neanderthal divergence (mclean et […]

2017
PMCID: 5499732

[…] in 65,772 final te copies belonging to 699 te families, which were assigned to only 658 families after two steps of clustering. clustering was performed using the three 80 criteria; manually through blat alignments, and automatically using cd-hit v4.5.4 (same parameters as in gene annotation). these 658 families were divided into five categories, following repbase classification (jurka et al. […]

2017
PMCID: 5299747

[…] and regulatory variation in hemoglobin genes, and then to determine their effects on physiology, environmental adaptation and disease., we used the basic local alignment search tool (blast) the blast-like alignment tool, and ncbi and ucsc genome [47–50] browsers to map the dog and cat hemoglobin genes querying with human and other mammalian genes and proteins. protein alignments were done […]

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

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