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BLAST-EXPLORER helps you building datasets for phylogenetic analysis.

Dereeper A, Audic S, Claverie JM, Blanc G - BMC Evol. Biol. (2010)

Bottom Line: To 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.BLAST-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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Information Génomique & Structurale-CNRS-UPR2589, Institut de Microbiologie de la Méditerranée-IFR 88, Marseille, France.

ABSTRACT

Background: The 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.

Results: To 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.

Conclusions: BLAST-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.

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BLAST-Explorer main interface. BLAST-Explorer main interface showing the similarity tree (A), hit descriptions (B), a coverage diagram representing the alignment of the hit sequences on the query (C), the taxonomy color code (D), individual BLAST pairwise alignments (E), the small-scale (F) and large-scale (H) selection tool panels. The "Score histogram" tool (G) and "Selection on taxonomy" tool (I) are given as examples.
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Figure 1: BLAST-Explorer main interface. BLAST-Explorer main interface showing the similarity tree (A), hit descriptions (B), a coverage diagram representing the alignment of the hit sequences on the query (C), the taxonomy color code (D), individual BLAST pairwise alignments (E), the small-scale (F) and large-scale (H) selection tool panels. The "Score histogram" tool (G) and "Selection on taxonomy" tool (I) are given as examples.

Mentions: By default, the result page only shows the top-100 scoring BLAST hits, while the remaining hits are kept in memory and can be activated using the large-scale selection tools (next section). Small-scale selection tools only apply on the top-100 scoring BLAST hits. The central tool in this mode is the sequence similarity tree that provides an approximate picture of the phylogenetic relationships between the query and the top BLAST hits (Fig. 1A). BLAST hits are renamed according to the species name. The similarity tree is documented with meta-information including hit description (Fig. 1B), alignment coverage (Fig. 1C), taxonomy-based coloring (Fig. 1D). The tree image allows a navigation across the BLAST result page (clicking on an alignment coverage bar [Fig. 1C] leads to the corresponding pairwise alignment [Fig. 1E]), gives access to the database record (by clicking on the hit name), as well as to the selection of individual hits (check-boxes) or in bulk (by clicking on internal branches).


BLAST-EXPLORER helps you building datasets for phylogenetic analysis.

Dereeper A, Audic S, Claverie JM, Blanc G - BMC Evol. Biol. (2010)

BLAST-Explorer main interface. BLAST-Explorer main interface showing the similarity tree (A), hit descriptions (B), a coverage diagram representing the alignment of the hit sequences on the query (C), the taxonomy color code (D), individual BLAST pairwise alignments (E), the small-scale (F) and large-scale (H) selection tool panels. The "Score histogram" tool (G) and "Selection on taxonomy" tool (I) are given as examples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2821324&req=5

Figure 1: BLAST-Explorer main interface. BLAST-Explorer main interface showing the similarity tree (A), hit descriptions (B), a coverage diagram representing the alignment of the hit sequences on the query (C), the taxonomy color code (D), individual BLAST pairwise alignments (E), the small-scale (F) and large-scale (H) selection tool panels. The "Score histogram" tool (G) and "Selection on taxonomy" tool (I) are given as examples.
Mentions: By default, the result page only shows the top-100 scoring BLAST hits, while the remaining hits are kept in memory and can be activated using the large-scale selection tools (next section). Small-scale selection tools only apply on the top-100 scoring BLAST hits. The central tool in this mode is the sequence similarity tree that provides an approximate picture of the phylogenetic relationships between the query and the top BLAST hits (Fig. 1A). BLAST hits are renamed according to the species name. The similarity tree is documented with meta-information including hit description (Fig. 1B), alignment coverage (Fig. 1C), taxonomy-based coloring (Fig. 1D). The tree image allows a navigation across the BLAST result page (clicking on an alignment coverage bar [Fig. 1C] leads to the corresponding pairwise alignment [Fig. 1E]), gives access to the database record (by clicking on the hit name), as well as to the selection of individual hits (check-boxes) or in bulk (by clicking on internal branches).

Bottom Line: To 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.BLAST-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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Information Génomique & Structurale-CNRS-UPR2589, Institut de Microbiologie de la Méditerranée-IFR 88, Marseille, France.

ABSTRACT

Background: The 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.

Results: To 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.

Conclusions: BLAST-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.

Show MeSH