BLAST: improvements for better sequence analysis

By Jian Ye, Scott D. McGinnis, Thomas L. Madden. 2006

724 citations recorded by the source corpus.

Basic local alignment search tool (BLAST) is a sequence similarity search program. The National Center for Biotechnology Information (NCBI) maintains a BLAST server with a home page at . We report here on recent enhancements to the results produced by the BLAST server at the NCBI. These include features to highlight mismatches between similar sequences, show where the query was masked for low-complexity sequence, and integrate information about the database sequences from the NCBI Entrez system into the BLAST display. Changes to how the database sequences are fetched have also improved the speed of the report generator.

Subfields: Molecular Biology

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Citations in the corpus

ECOD: An Evolutionary Classification of Protein Domains (2014, methodology): “Domains from the input chains could be classified by any combination of the three sequence-based methods (chain BLAST, domain BLAST, or domain HHsearch).”
BLAST: a more efficient report with usability improvements (2013, neutral): “(5) presented improvements to the alignment display.”
Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants (2020, methodology): “Next, for comparative modelling, BLAST [32] search identified SARS-CoV 3CLpro (PDB ID: 3M3V) as the best possible match in the PDB, with 100% query coverage, an E-value of 0.”
Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation (2009, methodology): “cgi) (Ye et al., 2006), and sequences with ambiguous BLAST matches were considered unclassified.”
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells (2011, methodology): “We generated non-coding RNA annotations by aligning their sequences to the mouse genome using BLAST 47 .”
Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota (2007, methodology): “The resulting phylotypes were then assigned similarities to nearest neighbours using BLAST.”
Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers (2009, methodology): “cgi) (59) using the PLAN system (24) to”
The BLAST Sequence Analysis Tool (2013, background): “The traceback then pulls the preliminary results from the SQL database and produces results that include insertions and deletions [8].”
NCBI BLAST: a better web interface (2008, background): “These formats are described in previous web server issues (7,8).”