BLAST-EXPLORER helps you building datasets for phylogenetic analysis

By A. Dereeper, S. Audic, Jean-Michel Claverie, Guillaume Le Blanc. BMC Evolutionary Biology, 2010

777 citations recorded by the source corpus.

BackgroundThe right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task.ResultsTo fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform.ConclusionsBLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bd02fb7758a584f1d3f95254014b7c751c3ae022

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In Ecology, Evolution, Behavior and Systematics

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Citations in the corpus

Review of octopamine in insect nervous systems (2012, neutral): “…of Evans and Maqueira (Figure 4B), 149 by adding another subclass in the tyraminergic class of receptors as shown in Figure 4C. 150,151 153–155 Based on nucleotide sequence homology in the phylogenetic tree, insect octopaminergic receptor sequences from the moth M. sexta (MsOA), 146…”
NGPhylogeny.fr: new generation phylogenetic services for non-specialists (2019, background): “Blast-Search is a successor of BlastExplorer (31), and uses BLAST (32) to retrieve and compare sequences that are similar enough to a user input sequence.”
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013, methodology): “Homologs for the six Megaviridae peptides were collected by keeping representative sequences among all detected taxonomic groups using BLAST-EXPLORER (Dereeper et al., 2010).”
Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes (2013, neutral): “fr [16,17].”