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Protocols

BFAST specifications

Information


Unique identifier OMICS_00652
Name BFAST
Alternative name BLAT-like Fast Accurate Search Tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/BFAST

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Documentation


Maintainer


  • person_outline Barry Merriman

Publication for BLAT-like Fast Accurate Search Tool

BFAST citations

 (79)
call_split

Rifampin modulation of xeno‐ and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes

2018
PMCID: 5869567
PMID: 29610665
DOI: 10.1002/prp2.386
call_split See protocol

[…] recalibration. Each sequence was scanned for low‐quality reads and any read length of less than 35 bases was discarded to effectively eliminate low‐quality reads while retaining high‐quality regions. BFAST was used as the primary sequence alignment algorithm employing a TopHat‐like strategy to align sequencing reads that crossed splicing junctions. Sequence reads were aligned to a filtering index […]

library_books

Molecular adaptations of adipose tissue to 6 weeks of morning fasting vs. daily breakfast consumption in lean and obese adults

2017
PMCID: 5813615
PMID: 29193093
DOI: 10.1113/JP275113

[…] muscle (Camera et al. ). Therefore, it could be that any potential change in PGC1α with our intermittent fasting protocol was offset by a difference in the physical activity patterns between FAST and BFAST groups.The large (>700 kcal) carbohydrate‐rich breakfast employed in the present study may preclude generalisation to smaller breakfasts differing in composition. However, the rationale for a la […]

call_split

Binding to RNA regulates Set1 function

2017
PMCID: 5654745
PMID: 29071121
DOI: 10.1038/celldisc.2017.40
call_split See protocol

[…] ughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Sequencing reads (FastQ format) were mapped to the Saccharomyces cerevisiae genome (sacCer3) using BFAST alignment tool with default parameters [] (PMID 19907642) to obtain a Binary Alignment Mapped (BAM) file. The sorted BAM files were used to determine average profiles of ChIP-Seq read density us […]

library_books

A Gene Module Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer

2017
Comput Struct Biotechnol J
PMCID: 5683705
PMID: 29158875
DOI: 10.1016/j.csbj.2017.09.003

[…] nd 1.6% Asian. The median age of patients at diagnosis is 60.9 years . The whole-exome sequencing reads from 417 of paired tumor and normal tissue samples were aligned to human reference genome using Blat-like Fast Accurate Search Tool (BFAST) . Then, genome-wide somatic mutations were detected using the MuTect algorithm . The RNA sequencing data was generated from 539 tumor and 72 matched normal […]

library_books

Current remote sensing approaches to monitoring forest degradation in support of countries measurement, reporting and verification (MRV) systems for REDD+

2017
PMCID: 5393981
PMID: 28417324
DOI: 10.1186/s13021-017-0078-9

[…] the signal, the unit change (e.g., percent) in a vegetation metric, relative to a reference condition, is estimated. One such approach is the pixel-based Break detection For Additive Seasonal Trends (BFAST) Monitor [], which models the expected behaviour of a time-series and identifies those pixels that deviate significantly as breakpoints. The magnitude of the detected change is related to the ty […]

library_books

Evaluating alignment and variant calling software for mutation identification in C. elegans by whole genome sequencing

2017
PLoS One
PMCID: 5363872
PMID: 28333980
DOI: 10.1371/journal.pone.0174446

[…] The following software were used for sequence alignment: BBMap [], BFAST [], Bowtie 2 [], BWA [] and NovoAlign [] The software used for variant calling were: FreeBayes [], GATK HaplotypeCaller [], SAMtools/BCFtools [], and VarScan 2 []. Additional software utilities […]

Citations

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BFAST institution(s)
Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
BFAST funding source(s)
Partially supported by University of California Systemwide Biotechnology Research and Education Program GREAT Training Grant 2007-10, the NIH Neuroscience Microarray Consortium (U24NS052108), a supplement to a grant from the NIMH (R01 MH071852) and the Dani Saleh Brain Tumor Fund.

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