BLAST: at the core of a powerful and diverse set of sequence analysis tools

By Scott D. McGinnis, Thomas L. Madden. Nucleic Acids Res., 2004

2,118 citations recorded by the source corpus.

Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a3ef0853c9d59d31f3da79583164120d93178a6f

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Citations in the corpus

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization (2006, methodology): “FASTSNP also uses NCBI BLAST (26) to search the UCSC Golden Path to extend the SNP sequence to 500 base-pairs.”
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006, methodology): “And, as shown previously, Sequence Match is more reliable than BLAST at retrieving the closest pairwise matches (1).”
NCBI BLAST: a better web interface (2008, background): “These formats are described in previous web server issues (7,8).”
BLAST: improvements for better sequence analysis (2006, background): “The Query-anchored view gives a stacked view of database sequences aligned to the query with indication of insertions and mismatches (3).”
The BLAST Sequence Analysis Tool (2013, background): “The Merger merges all pieces into one result which it stores in the SQL server [7].”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, neutral): “40 Two chains were assigned to the same cluster if the residue identity was (cid:1) 30% and (cid:1) 90% of the amino acids were aligned.”
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes (2014, methodology): “Standalone tools based on sequence similarity are also frequently used [27,28], with CD-HIT-EST a popular choice [29,30].”
Locating proteins in the cell using TargetP, SignalP and related tools (2007, methodology): “If pairwise identity is used as a measure of homology, the conclusion was that over 70% identical residues in a pairwise BLAST searc”
Dynamical networks in tRNA:protein complexes (2009, methodology): “horikoshii to perform BLAST searches (26) over the NCBI nonredundant database (27), with E value cutoff of 10 5 to construct the respective EPs.”
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads (2020, positive): “GMcloser and FGAP (based on BLAST [26]) and PBJelly (based on BLASR [45]) were the most time-consuming.”
Predicting protein function from sequence and structural data. (2005, methodology): “Typically, however, the sequence-based methods used are simple BLAST [8] or FASTA runs, which merely perform direct sequence-sequence comparisons.”