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. 2015 Aug 25:4:39.
doi: 10.1186/s13742-015-0080-7. eCollection 2015.

NCBI BLAST+ integrated into Galaxy

Peter J A Cock  1 , John M Chilton  2 , Björn Grüning  3 , James E Johnson  2 , Nicola Soranzo  4
Affiliations

NCBI BLAST+ integrated into Galaxy

Peter J A Cock et al. Gigascience. .

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.

Keywords: Accessibility; Annotation; BLAST; Galaxy; Pipeline; Reproducibility; Sequence analysis; Workflow.

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Figures

Fig. 1
Fig. 1
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
See this image and copyright information in PMC

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References

    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10. doi: 10.1016/S0022-2836(05)80360-2. - DOI - PubMed
    1. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12(10):1611–8. doi: 10.1101/gr.361602. - DOI - PMC - PubMed
    1. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25(11):1422–3. doi: 10.1093/bioinformatics/btp163. - DOI - PMC - PubMed
    1. Holland RCG, Down TA, Pocock M, Prlić A, Huen D, James K, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008;24(18):2096–7. doi: 10.1093/bioinformatics/btn397. - DOI - PMC - PubMed
    1. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010;26(20):2617–9. doi: 10.1093/bioinformatics/btq475. - DOI - PMC - PubMed

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