NCBI BLAST: a better web interface

By Mark Johnson, I. Zaretskaya, Yan Raytselis, Yuri Merezhuk, Scott D. McGinnis, Thomas L. Madden. Nucleic Acids Res., 2008

3,967 citations recorded by the source corpus.

Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/84ae10c7b36a113970ab846c8edb73eaff1ebca3

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Citations in the corpus

GPCRdb: an information system for G protein-coupled receptors (2015, background): “GPCRdb includes BLAST similarity search (27) to quickly find the most similar sequences for a user-provided query.”
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease (2011, methodology): “The resulting phylotypes were then assigned similarities to nearest neighbours using MegaBLAST [ 82 ].”
BLAST: a more efficient report with usability improvements (2013, background): “(3) presented an extensive redesign of the BLAST submission pages.”
Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants (2020, positive): “9 1 Next, for comparative modelling, BLAST [17] identified SARS-CoV 3CL (PDB ID: 3M3V) as the best possible match in the PDB, with 100% query coverage, an E-value of 0.”
Presenting your structures: the CCP4mg molecular-graphics software (2011, methodology): “This figure also demonstrates the new singlewindow appearance of CCP4mg, with the Sequence viewer, Display Table and Clip and Fog widgets docked in the main window. display any corresponding structures is also possible using the EBI/NCBI BLAST service (Johnson et al., 2008; McWilliam et al., 2009).”
GenBank (2012, methodology): “BLAST searches may be performed on the NCBI website (13) or by using a set of standalone programs distributed by FTP (4).”
GPCRdb: the G protein‐coupled receptor database – an introduction (2016, methodology): “The GPCRdb can be queried using BLAST (Johnson et al., 2008), and a specialized similarity search that utilizes custom segment selections (above) of the reference structure-based alignments.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “We then clustered all sequences [BlastClust(69)], annotated them with cluster size, modeling coverage and number of predicted transmembrane helices.”
NCBI Viral Genomes Resource (2014, methodology): “To restrict nucleotide Blast searches to include only viral RefSeq genomes, employ the ‘Choose Search Set’ options in the Blast search interface (55): Select ‘Reference genomic sequences (RefSeq genomic)’ in the database field and enter ‘Viruses’ in the ‘Organism’ field text box.”
Interactive metagenomic visualization in a Web browser (2011, methodology): “Figure 2, for example, shows an NCBI taxonomy summarized at a maximum depth of 6 levels and with linear subgraphs collapsed.”