BLAT pipeline

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


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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 <>

Publications for BLAST-Like Alignment Tool

BLAT IN pipelines

 (181)
2018
PMCID: 5791963
PMID: 29385200
DOI: 10.1371/journal.pone.0191205

[…] 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 […]

2018
PMCID: 5832876
PMID: 29497070
DOI: 10.1038/s41598-018-22093-3

[…] required to exhibit slts in at least one gene downstream of the first gene in the polycistronic unit. certain predictions were visually verified using igv 2.1 (broad institute)50., we performed a blat50 search (with -t = dna -q = dna -minidentity = 90 -out = blast8 –maxgap = 1 -fine parameters) on the s. mansoni genome for the 36 nt sl sequence. sl genes encoding the sl rna were identified […]

2018
PMCID: 5845709
PMID: 29559983
DOI: 10.3389/fpls.2018.00244

[…] acquired, conserved lncrnas were identified according to wheat lncrna dataset (ftp://ftp.ensemblgenomes.org/pub/plants/release-27/gtf/triticum_aestivum/triticum_aestivum.iwgsc1.0+popseq.27.gtf.gz), blat was used to submit to pfam database to remove potential coding transcripts, and 5,943 lncrnas were identified. among the 5,943 lncrnas, 131 were known lncrnas and 5,812 were novel lncrnas […]

2018
PMCID: 5906534
PMID: 29706951
DOI: 10.3389/fimmu.2018.00603

[…] ia, usa) was used to design two taqman assays against rv_007357 and a single assay against each of the remaining ltr12 elements. primer and probe sequences for these taqman assays were subject to blat analysis against the human genome to confirm specificity and are presented in table 1. five nanograms of rna in a 20 µl pcr reaction volume were used for each target in duplicate. the taqman […]

2018
PMCID: 5940156
PMID: 29540443
DOI: 10.1534/g3.118.200087

[…] was required to be considered a match to the barcode. sequences ≥50 bp after demultiplexing were kept for downstream analysis. sequences were aligned to human reference genome grch37 using pblat (blat in parallel setting) (http://icebert.github.io/pblat/) using the parameters stated in table s2 (kent 2002; wei and williams 2016). the performance of pblat was evaluated using 20,000 sequences […]

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

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