FAST statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FAST
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Tool usage distribution map

This map represents all the scientific publications referring to FAST per scientific context
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Protocols

FAST specifications

Information


Unique identifier OMICS_03640
Name FAST
Alternative name Fast Alignment and Search Tool
Interface Web user interface
Restrictions to use None
Input format PDB
Operating system Unix/Linux, Mac OS
Computer skills Basic
Stability Stable
Maintained No

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This tool is not available anymore.

Information


Unique identifier OMICS_03640
Name FAST
Alternative name Fast Alignment and Search Tool
Restrictions to use Academic or non-commercial use

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Publication for Fast Alignment and Search Tool

FAST citations

 (7)
library_books

Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors

2015
BMC Genomics
PMCID: 4413995
PMID: 25896665
DOI: 10.1186/s12864-015-1449-9

[…] calculate the average read depth from those libraries, reads were first aligned to the repeat masked reference genome (Sus scrofa build 10.2) using mrsFAST v2.3.0.2 (“Micro-read (substitutions only) fast alignment and search tool” []) with an edit distance of at most 7 given that the mean divergence between the seven species is maximum 2% [,]. Repeat masked information was obtained from NCBI (ref […]

library_books

Evaluation and Comparison of Multiple Aligners for Next Generation Sequencing Data Analysis

2014
Biomed Res Int
PMCID: 3980841
PMID: 24779008
DOI: 10.1155/2014/309650

[…] gether in the hash table-based algorithm include SeqMap [], PASS [], MAQ [], GASSST [], RMAP [], PerM [], RazerS [, ], microread Fast Alignment Search Tool (mrFAST) [], microread (substitutions only) Fast Alignment and Search Tool (mrsFAST) [], GenomeMapper [], and BOAT [].However, diverse strategies for seeds detection cause a distinction among multiple alignment algorithms. To handle the reads a […]

library_books

Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling

2013
PMCID: 3849742
PMID: 24079299
DOI: 10.1186/1757-4749-5-28

[…] y providing appropriate template structures (see 'Results and Discussion’). For checking the structural similarity, the homology models were superposed with the help of the freely available software 'FAST Alignment and Search Tool’ [] and RMSD value(s) were noted. […]

library_books

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

2013
BMC Genomics
PMCID: 3716681
PMID: 23829399
DOI: 10.1186/1471-2164-14-449

[…] ta. To calculate the average read depth from those libraries, reads were aligned to the available pig reference genome (Sus scrofa build 10.2) using mrsFAST v2.3.0.2 (“Micro-read (substitutions only) fast alignment and search tool” []) with an edit distance of at most 7. mrsFAST is a memory efficient and fast software, which reports all possible mapping locations (not only the best, unique or firs […]

call_split

Random Amino Acid Mutations and Protein Misfolding Lead to Shannon Limit in Sequence Structure Communication

2008
PLoS One
PMCID: 2518838
PMID: 18769673
DOI: 10.1371/journal.pone.0003110
call_split See protocol

[…] tire pool of NP with the smallest difference in sequence length among those sharing the same domain architecture in CATH. All identified pairs were then geometrically aligned with the FAST algorithm (Fast Alignment and Search Tool, ) yielding an all-atom alignment RMSD of 2.54±2.23 Å with a fraction of 0.63±0.32 of the residues aligned. Thus, on average, both chains were representatives of the sam […]

library_books

Accuracy of structure based sequence alignment of automatic methods

2007
BMC Bioinformatics
PMCID: 2039753
PMID: 17883866
DOI: 10.1186/1471-2105-8-355

[…] mbinatorial Extension; DaliLite, standalone version of DALI (Distance mAtrix ALIgnment); DSSP, Definition of Secondary Structure of Proteins given a set of 3D coordinates; FAST, Recursive acronym for FAST Alignment and Search Tool; FASTA3, DNA and Protein sequence alignment software package; LOCK2, Improvements over LOCK (Hierarchical protein structure superposition); MATRAS, MArkovian TRAnsition […]


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FAST institution(s)
Bioinformatics Program, Boston University, Boston, MA, USA; Biomedical Engineering Department, Boston University, Boston, MA, USA
FAST funding source(s)
Supported by the National Science Foundation, NSF DBI-0078194.

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