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NCBI BLAST+ integrated into Galaxy.

Cock PJ, Chilton JM, Grüning B, Johnson JE, Soranzo N - Gigascience (2015)

Bottom Line: The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses.This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide.Several examples of applications are described here.

View Article: PubMed Central - PubMed

Affiliation: Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK.

ABSTRACT

Background: The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows.

Findings: The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible.

Conclusions: This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.

No MeSH data available.


Related in: MedlinePlus

Galaxy workflow for finding gene clusters. Screenshot from the Galaxy Workflow Editor, showing a published example workflow [27] discussed in the Analyses section. Given two protein sequences, regions of a genome of interest are identified that contain tblastn matches to both sequences, which pinpoints candidate gene clusters for further study
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Fig1: Galaxy workflow for finding gene clusters. Screenshot from the Galaxy Workflow Editor, showing a published example workflow [27] discussed in the Analyses section. Given two protein sequences, regions of a genome of interest are identified that contain tblastn matches to both sequences, which pinpoints candidate gene clusters for further study

Mentions: For this application a workflow was constructed to query two translated protein sequences against a BLAST nucleotide database for the target genome [27] (Fig. 1). This workflow is available with sample data via the Galaxy Tool Shed [28] and myExperiment [29].Fig. 1


NCBI BLAST+ integrated into Galaxy.

Cock PJ, Chilton JM, Grüning B, Johnson JE, Soranzo N - Gigascience (2015)

Galaxy workflow for finding gene clusters. Screenshot from the Galaxy Workflow Editor, showing a published example workflow [27] discussed in the Analyses section. Given two protein sequences, regions of a genome of interest are identified that contain tblastn matches to both sequences, which pinpoints candidate gene clusters for further study
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4557756&req=5

Fig1: Galaxy workflow for finding gene clusters. Screenshot from the Galaxy Workflow Editor, showing a published example workflow [27] discussed in the Analyses section. Given two protein sequences, regions of a genome of interest are identified that contain tblastn matches to both sequences, which pinpoints candidate gene clusters for further study
Mentions: For this application a workflow was constructed to query two translated protein sequences against a BLAST nucleotide database for the target genome [27] (Fig. 1). This workflow is available with sample data via the Galaxy Tool Shed [28] and myExperiment [29].Fig. 1

Bottom Line: The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses.This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide.Several examples of applications are described here.

View Article: PubMed Central - PubMed

Affiliation: Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK.

ABSTRACT

Background: The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows.

Findings: The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible.

Conclusions: This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.

No MeSH data available.


Related in: MedlinePlus