NCBI BLAST+ integrated into Galaxy

GigaScience

Volumn 4, Issue 1, 2015, Pages

  Cock, Peter J A ^a   Chilton, John M ^b   Grüning, Björn ^c   Johnson, James E ^b   Soranzo, Nicola ^d  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF FREIBURG   (Germany)

^d CA ^*  (Italy)

Author keywords

Accessibility; Annotation; BLAST; Galaxy; Pipeline; Reproducibility; Sequence analysis; Workflow

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GALAXY PROJECT; GENE CLUSTER; GENOME; MOLECULAR BIOLOGY; NCBI BLAST; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEOMICS; SEQUENCE ANALYSIS; BIOLOGY; INTERNET; NATIONAL HEALTH ORGANIZATION; UNITED STATES;

COMPUTATIONAL BIOLOGY; INTERNET; NATIONAL INSTITUTES OF HEALTH (U.S.); UNITED STATES;

EID: 84979555726     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/s13742-015-0080-7     Document Type: Article

References (41)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10
2. 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
3. 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
4. Holland RCG, Down TA, Pocock M, Prlic A, Huen D, James K, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008;24(18):2096-7
5. 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
6. Goecks J, Nekrutenko A, Taylor J. The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86
7. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. Curr Protoc Mol Biol. 2010;19:19.10.1-19.10.21. doi:10.1002/0471142727. mb1910s89
8. Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, et al. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010;38 suppl 2:W677-82
9. Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, et al. Dissemination of scientific software with Galaxy ToolShed. Genome Biol. 2014;15(2):403
10. Cock PJA, Grüning BA, Paszkiewicz K, Pritchard L. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. Peer J. 2013;1:e167
11. Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 2014;42(W1):W187-91
12. Aranguren ME, Breis JTF, Antezana E, Mungall C, Gonzalez AR, Wilkinson M. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. J Biomed Semantics. 2013;4(1):2
13. Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, et al. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 2014;30(13):1928-9
14. Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J. Galaxy CloudMan: delivering cloud compute clusters. BMC Bioinformatics. 2010;11 Suppl 12:S4
15. Grau J, Boch J, Posch S. TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics. 2013;29(22):2931-2
16. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421-9
17. Keller O, Kollmar M, Stanke M, Waack S. A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics. 2011;27(6):757-63
18. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673-9
19. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068-9
20. Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxonannotated GC-coverage plots. Front Genet. 2013;4:237
21. Galaxy Tool Shed Repository "clc_assembly_cell": https://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell/
22. Galaxy Tool Shed Repository "blast_top_hit_species": https://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species/
23. myExperiment Species of top BLAST hits: http://www.myexperiment.org/workflows/4637.html
24. Yong E. There's No Plague on the NYC Subway. No Platypuses Either. National Geographic Magazine, Phenomena: Not Exactly Rocket Science; 2015: http://phenomena.nationalgeographic.com/2015/02/10/theres-noplague-on-the-nyc-subway-no-platypuses-either/
25. Galaxy Tool Shed Repository "Filter sequences by ID": https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/
26. Fischbach M, Voigt CA. Prokaryotic gene clusters: A rich toolbox for synthetic biology. Biotechnol J. 2010;5(12):1277-96
27. Präg A, Grüning BA, Häckh M, Lüdeke S, Wilde M, Luzhetskyy A, et al. Regioand stereoselective intermolecular oxidative phenol coupling in Streptomyces. J Am Chem Soc. 2014;136(17):6195-8
28. Galaxy Tool Shed Repository "find_genes_located_nearby_workflow": https://toolshed.g2.bx.psu.edu/view/bgruening/find_genes_located_nearby_workflow/
29. myExperiment Galaxy workflow for the identification of candidate genes clusters: http://www.myexperiment.org/workflows/4584.html
30. Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, et al. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. 2014;13(12):5898-908
31. Travis CI Galaxy code and wrappers: https://travis-ci.org/peterjc/galaxy_blast
32. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa/Illumina FASTQ Variants. Nucleic Acids Res. 2010;38(6):1767-71
33. Grüning B, Cock PJA. docker-galaxy-blast: The NCBI Blast + 2.2.29 release. 2015. doi:10.5281/zenodo.15781
34. NCBI BLAST databases: ftp://ftp.ncbi.nlm.nih.gov/blast/db/
35. Blankenberg D, Johnson JE, Taylor J, Nekrutenko A, The Galaxy Team. Wrangling Galaxy's reference data. Bioinformatics. 2014;30(13):1917-9
36. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-409
37. Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001;29(14):2994-3005
38. Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004;32 suppl 2:W327-31
39. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011;39 suppl 1:D225-9
40. Goecks J, Eberhard C, Too T, Nekrutenko A, Taylor J, The Galaxy Team. Webbased visual analysis for high-throughput genomics. BMC Genomics. 2013;14:397
41. Cock PJA, Chilton JM, Grüning B, Johnson JE, Soranzo N. Supporting data and materials for "NCBI BLAST+ integrated into Galaxy". GigaScience Database. 2015. http://dx.doi.org/10.5524/100149