NCBI BLAST+ integrated into Galaxy

Peter J.A. Cock; John M. Chilton; Björn Grüning; James E. Johnson; Nicola Soranzo

doi:10.1186/s13742-015-0080-7

NCBI BLAST+ integrated into Galaxy

Peter J.A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo

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154 Scopus citations

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.

Original language	English (US)
Article number	39
Journal	GigaScience
Volume	4
Issue number	1
DOIs	https://doi.org/10.1186/s13742-015-0080-7
State	Published - 2015

Bibliographical note

Funding Information:
We thank the NCBI BLAST team for their long-running work, the Galaxy team for their assistance and advice, the Galaxy community for their feedback and suggestions, and the past, present and future contributors to the Galaxy tools described here. Specifically, we thank Dannon Baker, Daniel Blankenberg, Edward Kirton, Kanwei Li and Luobin Yang. The three reviewers are thanked for their constructive feedback: Tom Madden, Gianmauro Cuccuru and, in particular, Stian Soiland-Reyes for his attention to detail. PJAC was funded by the Scottish Government’s Rural and Environment Science and Analytical Services (RESAS) Division. BAG was funded by the DFG CRC 992 Medical Epigenetics. JMC and JEJ were supported in part by NSF grant 1147079.

Funding Information:
PJAC was funded by the Scottish Government's Rural and Environment Science and Analytical Services (RESAS) Division. BAG was funded by the DFG CRC 992 Medical Epigenetics. JMC and JEJ were supported in part by NSF grant 1147079.

Keywords

Accessibility
Annotation
BLAST
Galaxy
Pipeline
Reproducibility
Sequence analysis
Workflow

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10.1186/s13742-015-0080-7

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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.",

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NCBI BLAST+ integrated into Galaxy

Abstract

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Keywords

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